bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative theory of telomere length regulation and cellular senescence
Authors: Rodriguez-Brenes Ignacio A. , Peskin Charles S.
Published: March 2010

In normal somatic cells, telomere length shortens with each cell replication. This progressive shortening is associated with cellular senescence and apoptosis. Germ cells, stem cells, and the majority of cancer cells express telomerase, an enzyme that extends telomere length and, when expressed at sufficient levels, can immortalize or extend the life span of a cell line. It is believed that telomeres switch between two states: capped and uncapped. The telomere state determines its accessibility to telomerase and also the onset of senescence. One hypothesis is that the t loop, a large lariat-like structure, represents the capped state. In this paper we model a telomere state on the basis of the biophysics of t-loop formation, allowing us to develop a single mathematical model that accounts for two processes: telomere length regulation for telomerase positive cells and cellular senescence in somatic cells. The model predicts the steady-state length distribution for telomerase positive cells, describes the time evolution of telomere length, and computes the life span of a cell line on the basis of the levels of TRF2 and telomerase expression. The model reproduces a wide range of experimental behavior and fits data from immortal cell lines (HeLa S3 and 293T) and somatic cells (human diploid fibroblasts) well. We conclude that the t loop as the capped state is a quantitatively reasonable model of telomere length regulation and cellular senescence.
Fast excitation of EGAM by NBI
Authors: Berk H.L. , Zhou T.
Published: March 2010

A new mechanism for the fast excitation of the energetic geodesic acoustic mode (EGAM) is proposed to explain the recent experiment in DIII-D (Nazikian et al 2008 Phys. Rev. Lett.
101 185001), where the mode turns on in less than a millisecond after the turn-on of the neutral beam injection. The existence of loss boundary in pitch angle when beam particles are injected counter to the plasma current is crucial to the formation of negative energy EGAM mode. The resonance of this negative energy wave with energetic particles, whose distribution decreases with energy, destabilizes the mode. We find that when there is a loss region, the onset time of instability can be significantly shorter than it would be if the injected particles had no loss region.
A parametric model for fusion neutron emissivity tomography for the KN3 neutron camera at JET
Authors: Ronchi E. , Conroy S. , Sundén E. Andersson , Ericsson G. , Johnson M. Gatu , Hellesen C. , Sjöstrand H. , Weiszflog M.
Published: March 2010

A parametric model for fusion neutron emissivity is presented and applied to the KN3 neutron camera data collected during the trace tritium experiment at the Joint European Torus. This work is aimed at achieving a good compromise between accuracy of tomographic reconstruction and low model complexity. This means low numerical degeneracy and good time consistency of the results. The model is compared both with plasma simulation codes and other tomographic techniques, which use KN3 line integrated emissivity data, showing good agreement over the entire data set analysed (≈500 plasma discharges).
Penetration characteristics of supersonic molecular beam injection on HL-2A tokamak
Authors: Yu D.L. , Chen C.Y. , Yao L.H. , Feng B.B. , Han X.Y. , Yang L.M. , Zhong W.L. , Zhou Y. , Zhao K.J. , Huang Y. , Liu Yi , Yan L.W. , Yang Q.W. , Dong J.Q. , Duan X.R.
Published: March 2010

The penetration characteristics of supersonic molecular beam injection (SMBI) have been studied on the HL-2A tokamak. The signals from the tangential Dα array and CCD camera clearly show that the SMBI from the low field side consists of a slow component (SC) and a fast component (FC) because of a small percentage of H2 present in the D2 reservoir. The FC can penetrate more deeply than the SC, e.g. 8.5 cm inside the last closed flux surface, while the SC is around 4 cm. The penetration depth of the SMBI is weakly dependent on plasma parameters before injection and its backing pressure. Fuelling efficiency of SMBI is also estimated because it is one of the key issues in fusion plasmas. Typical fuelling efficiency of SMBI is 30–60% for the limiter configuration on the HL-2A tokamak. The variation of the decay time of the post-SMBI electron density is more responsible for the large scatter of the measured fuelling efficiencies than the different injection depths.
Neutron production in ultraintense laser interactions with carbon-deuterated plasma at intensities of 1018 W cm−2
Authors: Youssef A. , Kodama R.
Published: March 2010

Wide-range neutron energy spectra that are produced when an ultraintense laser with an intensity of 3 × 1018 W cm−2 is focused on a CD2 target have been studied. The experimentally observed spectra and numerically calculated ones, by a three-dimensional Monte Carlo code, indicate that the energy range of the emitted neutrons is larger than that of the D(d,n)3He reaction. The reactions that can participate in neutron production and their relative importance have been analysed. An explanation for the measured spectra is introduced by taking into account the 12C(d,n)13N and D(12c,n)13N reactions. These reactions strongly participate in neutron production due to their high cross sections. Moreover, the neutrons from these reactions will overlap the neutrons from the D(d,n)3He reaction, including the 2.45 MeV neutrons, with increasing energy of the accelerated ions under higher irradiances.
Experimental simulation of ITER rampdown in DIII-D
Authors: Politzer P.A. , Jackson G.L. , Humphreys D.A. , Luce T.C. , Hyatt A.W. , Leuer J.A.
Published: March 2010

Because of the high value of the stored energy in planned ITER plasmas, the safe and controlled termination of ITER discharges is an important aspect of ITER operation. In a series of experiments on the DIII-D tokamak, we have simulated the proposed ITER rampdown for the 15 MA baseline operating scenario. These scaled discharges match the reference scenario (including scaled time dependence) with regard to key parameters such as scaled current, poloidal beta, elongation and internal inductance. The scaled plasma current is reduced to the equivalent of less than 1 MA, well below the 1.4 MA specified for ITER as the maximum allowable for disruptive termination. The plasma shape and position are controlled during rampdown so that the high heat flux zones near the strike points of the separatrix are held within the equivalent of the armoured zones of the ITER divertor; the regulation of the strike-point location is an order of magnitude better than required. Scans of the current rampdown rates indicate that a more rapid rampdown than the ITER reference case may be needed to avoid excessive current in the ITER central solenoid. Rampdown with a full-size plasma was studied, but was found to be unsuitable for ITER because of transitions to ELM-free H-mode with a consequent lack of density control, as well as large excursions in poloidal beta and internal inductance. We find that ELMs play an important role during the H-mode phase of the rampdown, helping to reduce the density as the current is reduced.
A very fast and accurate method for calling aberrations in array-CGH data
Authors: Benelli Matteo , Marseglia Giuseppina , Nannetti Genni , Paravidino Roberta , Zara Federico , Bricarelli Franca Dagna , Torricelli Francesca , Magi Alberto
Published: March 2010

Array comparative genomic hybridization (aCGH) is a microarray technology that allows one to detect and map genomic alterations. The standard workflow of the aCGH data analysis consists of 2 steps: detecting the boundaries of the regions of changed copy number by means of a segmentation algorithm (break point identification) and then labeling each region as loss, neutral, or gain with a probabilistic framework (calling procedure). In this paper, we introduce a novel calling procedure based on a mixture of truncated normal distributions, named FastCall, that aims to give aberration probabilities to segmented aCGH data in a very fast and accurate way. Both on synthetic and real aCGH data, FastCall obtains excellent performances in terms of classification accuracy and running time.
Particle dynamics inside shocks in Hamilton–Jacobi equations
Authors: Khanin Konstantin , Sobolevski Andrei
Published: March 2010

The characteristic curves of a Hamilton–Jacobi equation can be seen as action-minimizing trajectories of fluid particles. For non-smooth ‘viscosity’ solutions, which give rise to discontinuous velocity fields, this description is usually pursued only up to the moment when trajectories hit a shock and cease to minimize the Lagrangian action. In this paper we show that, for any convex Hamiltonian, there exists a uniquely defined canonical global non-smooth coalescing flow that extends particle trajectories and determines the dynamics inside shocks. We also provide a variational description of the corresponding effective velocity field inside shocks, and discuss the relation to the ‘dissipative anomaly’ in the limit of vanishing viscosity.
Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives
Authors: Otsuka Yuichiro , Muramatsu Yuki , Nakagawa Yasuyoshi , Matsuda Motoki , Nakamura Masaya , Murata Hitoshi
Published: March 2010

A novel bacterium, designated strain OX-01T, was isolated from acidic soil, taxonomically investigated and identified as an agent that catabolizes (+)-catechin into taxifolin. Strain OX-01T is a Gram-reaction-negative, aerobic, non-sporulating, non-motile and rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia and occupying a phylogenetic position closest to, but clearly distinct from, Burkholderia sacchari. Strain OX-01T does not have any nif genes, which are required for N2-fixation, in its genome, a feature that is similar to B. sacchari, which lacks nifH, but is distinct from the N2-fixing features of many other phylogenetically related taxa, such as Burkholderia ferrariae, B. heleia, B. mimosarum, B. nodosa, B. silvatlantica, B. tropica and B. unamae. Strain OX-01T has the following chemotaxonomic characteristics: the major ubiquinone is Q-8, the DNA G+C content is 64 mol% and the major fatty acids are C16 : 0, C17 : 0 cyclo and C18 : 1
ω7c. It also has a unique profile of carbohydrate utilization among other species of the genus Burkholderia. The strain cannot assimilate many pentoses, hexoses and oligosaccharides, whereas it can catabolize (+)-catechin and its putative aromatic derivatives, such as 4-hydroxy-3-methoxycinnamic acid, protocatechuic acid, p-hydroxybenzoic acid, trans-p-coumaric acid and vanillic acid. Based on its morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA relatedness values and 16S rRNA gene sequence comparison data, we show that strain OX-O1T represents a novel species of the genus Burkholderia, for which the name Burkholderia oxyphila sp. nov. is proposed. The type strain is OX-01T (=NBRC 105797T =DSM 22550T).
Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil
Authors: Yu Xin-Yan , Li Yong-Feng , Zheng Jin-Wei , Li Yi , Li Lian , He Jian , Li Shun-Peng
Published: March 2010

A bacterial strain, designated BF-3T, was isolated from phenol-contaminated soil and investigated using a polyphasic taxonomic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BF-3Tformed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genusComamonas; it showed highest sequence similarities toComamonas aquaticaLMG 2370T(96.8 %),C. nitrativoransDSM 13191T(96.4 %),C. odontotermitisLMG 23579T(96.4 %),C. kerstersiiLMG 3475T(96.3 %),C. koreensisKCTC 12005T(96.1 %) andC. terrigenaLMG 1253T(96.0 %). The major cellular fatty acids were C16 : 0, C18 : 1/C18 : 1ω7c, C17 : 0cyclo and summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain BF-3Twas clearly distinct from type strains of other recognized species of the genusComamonasand, as such, represents a novel species of the genusComamonas, for which the nameComamonas zonglianiisp. nov. is proposed. The type strain is BF-3T(=CCTCC AB 209170T=DSM 22523T).
Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete
Authors: Kim Sung M. , Park Sae W. , Park Sang T. , Kim Young M.
Published: March 2010

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).
Jeotgalicoccus coquinae sp. nov. and Jeotgalicoccus aerolatus sp. nov., isolated from poultry houses
Authors: Martin E. , Klug K. , Frischmann A. , Busse H.-J. , Kämpfer P. , Jäckel U.
Published: March 2010

Two Gram-stain-positive, non-motile, non-spore-forming cocci (strains MK-7T and MPA-33T) were isolated from poultry houses. Strain MK-7T was isolated on marine broth agar from coquina, a food supplement for female ducks used in a duck-fattening farm. Strain MPA-33T was isolated from the air of a turkey house on TSA after filter sampling. On the basis of 16S rRNA gene sequence similarity studies, both strains were shown to belong to the genus Jeotgalicoccus; MK-7T was most closely related to Jeotgalicoccus psychrophilus YKJ-115T (99.3 % similarity) and MPA-33T was most closely related to Jeotgalicoccus halotolerans YKJ-101T (98.8 %). The quinone system of MK-7T was composed of equal amounts of menaquinones MK-7 and MK-6 and that of MPA-33T contained 76 % MK-7 and 24 % MK-6. The polar lipid profile of strain MK-7T consisted of the major compounds diphosphatidylglycerol and phosphatidylglycerol and six unidentified lipids present in minor to moderate amounts. In strain MPA-33T, diphosphatidylglycerol was the single predominant lipid, whereas phosphatidylglycerol was detected in moderate amounts. In addition, one unidentified phospholipid and four unidentified lipids were detected. Fatty acid profiles with iso-15 : 0 and anteiso-15 : 0 as major fatty acids supported the affiliation of the strains to the genus Jeotgalicoccus. The results of physiological and biochemical tests as well as DNA–DNA hybridizations allowed clear phenotypic differentiation of strains MK-7T and MPA-33T from the most closely related species. Strains MK-7T and MPA-33T therefore represent novel species, for which the names Jeotgalicoccus coquinae sp. nov. (type strain MK-7T =DSM 22419T =CCM 7682T =CCUG 57956T) and Jeotgalicoccus aerolatus sp. nov. (type strain MPA-33T =DSM 22420T =CCM 7679T =CCUG 57953T) are proposed.
Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce
Authors: Namwong Sirilak , Tanasupawat Somboon , Kudo Takuji , Itoh Takashi
Published: March 2010

Two red-pigmented, strictly aerobic, pleomorphic rod-shaped and extremely halophilic archaea, designated strains HST01-2RTand HST03T, were isolated from salt in a fish sauce sample from Thailand. The novel strains grew optimally at 37 °C, pH 7.0, and in the presence of 20–25 % (w/v) NaCl. The DNA G+C contents of the isolates were 61.6–62.2 mol%. Phylogenetic analysis based on a comparison of 16S rRNA gene sequences revealed that strains HST01-2RTand HST03Twere placed in the radiation of species of the genusHaloarcula. The chemotaxonomic properties of the two strains, i.e. the presence of MK-8 and MK-8(H2) as the major menaquinone components and C20C20derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a triglycosyl diether as major polar lipids, supported the assignment of the two strains to the genusHaloarcula. Nevertheless, several phenotypic features and the low DNA–DNA relatedness between the two strains and related species of the genusHaloarcula(13.4–46.9 %) enabled the strains to be distinguished from each other and from recognized species. Therefore, strains HST01-2RTand HST03Trepresent two novel species in the genusHaloarcula, for which the namesHaloarcula salariasp. nov. andHaloarcula tradensissp. nov. are proposed, respectively. The type strains are HST01-2RT(=BCC 40029T=JCM 15759T=PCU 313T) and HST03T(=BCC 40030T=JCM 15760T=PCU 314T).
Candida andamanensis sp. nov., Candida laemsonensis sp. nov. and Candida ranongensis sp. nov., anamorphic yeast species isolated from estuarine waters in a Thai mangrove forest
Authors: Am-In Somjit , Limtong Savitree , Yongmanitchai Wichien , Jindamorakot Sasitorn
Published: March 2010

Five strains (RV5T, RV140, R31T, RS17 and RS28T) representing three novel anamorphic ascomycetous yeast species were isolated by membrane filtration from estuarine waters collected from a mangrove forest in Laem Son National Park, Ranong Province, Thailand, on different occasions. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and the internal transcribed spacer region and phylogenetic analysis, three strains were found to represent two novel Candida species. Two strains (RV5T and RV140) represented a single novel species, for which the name Candida laemsonensis sp. nov. is proposed. The type strain is RV5T (=BCC 35154T =NBRC 105873T =CBS 11419T). Strain R31T was assigned to a novel species that was named Candida andamanensis sp. nov. (type strain R31T =BCC 25965T =NBRC 103862T =CBS 10859T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and phylogenetic analysis, strains RS17 and RS28T represented another novel species of Candida, for which the name Candida ranongensis sp. nov. is proposed. The type strain is RS28T (=BCC 25964T =NBRC 103861T =CBS 10861T).
Novosphingobium soli sp. nov., isolated from soil
Authors: Kämpfer Peter , Young Chiu-Chung , Busse Hans-Jürgen , Lin Shi-Yao , Rekha P. D. , Arun A. B. , Chen Wen-Ming , Shen Fo-Ting , Wu Y.-H.
Published: March 2010

A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium, strain CC-TPE-1T, was isolated from oil-contaminated soil near an oil refinery located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis of strain CC-TPE-1T showed highest sequence similarity to Novosphingobium naphthalenivorans TUT562T (98.1 %), N. panipatense SM16T (97.9 %) and N. mathurense SM117T (97.6 %) and lower (<97 %) sequence similarity to all other Novosphingobium species. DNA–DNA hybridizations of strain CC-TPE-1T with N. naphthalenivorans DSM 18518T, N. panipatense SM16T and N. mathurense SM117T showed low relatedness of 30 % (reciprocal 35 %), 29.1 % (reciprocal 30.6 %) and 35 % (reciprocal 23.6 %), respectively. The major respiratory quinone was ubiquinone Q-10, the predominant fatty acid was C18 : 1
ω7c (49.9 %) and three 2-hydroxy fatty acids, C14 : 0 2-OH (8.2 %), C15 : 0 2-OH (2.45 %) and C16 : 0 2-OH (1.05 %), were detected. Polar lipids consisted mainly of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, two sphingoglycolipids, phosphatidylmonomethylethanolamine and several unidentified lipids, and a yellow pigment was also detected. The polyamine pattern contained the single major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain CC-TPE-1T represents a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium soli sp. nov., with the type strain CC-TPE-1T (=DSM 22821T =CCM 7706T =CCUG 58493T).
Differential Oxidative Metabolism and 5-Ketoclomazone Accumulation Are Involved in Echinochloa phyllopogon Resistance to Clomazone
Authors: Yasuor Hagai , Zou Wei , Tolstikov Vladimir V. , Tjeerdema Ronald S. , Fischer Albert J.
Published: March 2010

Echinochloa phyllopogon (late watergrass) is a major weed of California rice (Oryza sativa) that has evolved cytochrome P450-mediated metabolic resistance to different herbicides with multiple modes of action. E. phyllopogon populations from Sacramento Valley rice fields have also recently shown resistance to the herbicide clomazone. Clomazone is a proherbicide that must be metabolized to 5-ketoclomazone, which is the active compound that inhibits deoxyxylulose 5-phosphate synthase, a key enzyme of the nonmevalonate isoprenoid pathway. This study evaluated the differential clomazone metabolism within strains of the same species to investigate whether enhanced oxidative metabolism also confers clomazone resistance in E. phyllopogon. Using reverse-phase liquid chromatography-tandem mass spectrometry techniques in the multireaction monitoring mode, we elucidated that oxidative biotransformations are involved as a mechanism of clomazone resistance in this species. E. phyllopogon plants hydroxylated mostly the isoxazolidinone ring of clomazone, and clomazone hydroxylation activity was greater in resistant than in susceptible plants. The major clomazone metabolites resulted from monohydroxylation and dihydroxylation of the isoxazolidinone ring. Resistant plants accumulated 6- to 12-fold more of the monohydroxylated metabolite than susceptible plants, while susceptible plants accumulated 2.5-fold more of the phytotoxic metabolite of clomazone, 5-ketoclomazone. Our results demonstrate that oxidative metabolism endows multiple-herbicide-resistant E. phyllopogon with cross-resistance to clomazone through enhanced herbicide degradation and lower accumulation of the toxic metabolite in resistant versus susceptible plants.
Mathematical Modeling of the Central Carbohydrate Metabolism in Arabidopsis Reveals a Substantial Regulatory Influence of Vacuolar Invertase on Whole Plant Carbon Metabolism
Authors: Nägele Thomas , Henkel Sebastian , Hörmiller Imke , Sauter Thomas , Sawodny Oliver , Ederer Michael , Heyer Arnd G.
Published: March 2010

A mathematical model representing metabolite interconversions in the central carbohydrate metabolism of Arabidopsis (Arabidopsis thaliana) was developed to simulate the diurnal dynamics of primary carbon metabolism in a photosynthetically active plant leaf. The model groups enzymatic steps of central carbohydrate metabolism into blocks of interconverting reactions that link easily measurable quantities like CO2 exchange and quasi-steady-state levels of soluble sugars and starch. When metabolite levels that fluctuate over diurnal cycles are used as a basic condition for simulation, turnover rates for the interconverting reactions can be calculated that approximate measured metabolite dynamics and yield kinetic parameters of interconverting reactions. We used experimental data for Arabidopsis wild-type plants, accession Columbia, and a mutant defective in vacuolar invertase, AtβFruct4, as input data. Reducing invertase activity to mutant levels in the wild-type model led to a correct prediction of increased sucrose levels. However, additional changes were needed to correctly simulate levels of hexoses and sugar phosphates, indicating that invertase knockout causes subsequent changes in other enzymatic parameters. Reduction of invertase activity caused a decline in photosynthesis and export of reduced carbon to associated metabolic pathways and sink organs (e.g. roots), which is in agreement with the reported contribution of vacuolar invertase to sink strength. According to model parameters, there is a role for invertase in leaves, where futile cycling of sucrose appears to have a buffering effect on the pools of sucrose, hexoses, and sugar phosphates. Our data demonstrate that modeling complex metabolic pathways is a useful tool to study the significance of single enzyme activities in complex, nonintuitive networks.
bZIP28 and NF-Y Transcription Factors Are Activated by ER Stress and Assemble into a Transcriptional Complex to Regulate Stress Response Genes in Arabidopsis
Authors: Liu Jian-Xiang , Howell Stephen H.
Published: March 2010

Stress agents known to elicit the unfolded protein response in Arabidopsis thaliana upregulate the expression of a constellation of genes dependent on the membrane-associated basic domain/leucine zipper (bZIP) transcription factor, bZIP28. Among the stress-activated genes, a consensus promoter sequence corresponding to the endoplasmic reticulum (ER) stress-responsive element I (ERSE-I), CCAAT-N10-CACG, was identified. Disruption of either the CCAAT or CACG subelement in ERSE-I resulted in reduction of the transcriptional response to ER stress. bZIP28 forms homo- and heterodimers with other bZIP TF family members (in subgroup D) and interacts with CCAAT box binding factors, heterotrimeric factors composed of NF-Y subunits. Arabidopsis encodes 36 NF-Y subunits, and it was found that subunits NF-YB3 and -YC2 interact with bZIP28 and NF-YA4, respectively, in a yeast three-hybrid system. A transcriptional complex containing bZIP28 and the above-mentioned three NF-Y subunits was assembled in vitro on DNA containing ERSE-I. bZIP28, on its own, binds to the CACG subelement in ERSE-I to form a smaller complex I, and in combination with the NF-Y subunits above, bZIP28 assembles into a larger transcriptional complex (complex II). bZIP28 was shown to interact with NF-Y subunits in vivo in bimolecular fluorescence complementation analyses and in coimmunoprecipitation assays. Treatment of seedlings with ER stress agents led to the upregulation of NF-YC2 and the relocation of NF-YB3 from the cytoplasm to the nucleus. Thus, in response to ER stress, bZIP28 is mobilized by proteolysis and recruits NF-Y subunits to form a transcriptional complex that upregulates the expression of ER stress-induced genes.
Quantitative analysis of the effect of coarse aggregate diffusivity on reinforcing steel corrosion initiation with a finite element model
Authors: Yu Hui , Hartt William H.
Published: March 2010

Purpose

The purpose of this paper is to explore and compare the influence of diverse coarse aggregate (CA) diffusivities on reinforcing steel corrosion initiation through a quantitative modeling analysis approach.

Design/methodology/approach

Finite element analysis was used to solve two‐dimensional chloride diffusion processes, which follow the Fick's second law within the concrete cover. Two non‐dimensional time‐derating factors were employed to quantify the time‐to‐corrosion of steel rebar, Ti, for different models.

Findings

The finite diffusivity CA exhibits variable effects on Ti, depending upon: diffusivity ratio between the CA and mortar; CA type; reinforcement corrosion resistance; and cover thickness. The intent of the effects are expressed quantitatively and their implications discussed.

Originality/value

The methodology and results presented in this paper provide insights on the variable reinforcement Ti values as a function of CA diffusivity. The approach employed herein provides an effective tool to select CA materials for reinforced concrete structure where chloride‐induced corrosion is a concern.
Stress corrosion cracking of sensitized austenitic stainless steels in Kuwait petroleum refineries
Authors: Almubarak A. , Belkharchouche M. , Hussain A.
Published: March 2010

Purpose

The purpose of this paper is to investigate stress corrosion cracking (SCC) for 304, 316, and 321 stainless steels in petroleum‐processing environments.

Design/methodology/approach

Sensitized austenitic stainless steels were subjected to a microstructure investigation and electrochemical test. Stressed sensitized 304, 316, and 321 stainless steels were selected and subjected to various environments that included polythionic acid, sour solution, and chloride solution that were prepared in the laboratory to simulate service environments in the petroleum refinery.

Findings

Microstructure investigation reveals more severe SCC in polythionic acid than in the sour and chloride solutions. Type 321 SS gives better resistance to SCC than do 304 and 316 SS in the three solutions. It is concluded that acidity of solutions has a relatively minor influence in promoting cracking. However, polythionic acid is found to be the primary causative agent.

Originality/value

The results demonstrated that SCC is more severe in polythionic acid than in chloride and sour solutions.
Application of the inverse wavelet transform on electrochemical current signals to demonstrate the essence of high‐frequency variations
Authors: Khodayari Mehdi , Reza Allahkaram Saeed , Volinsky Alex A.
Published: March 2010

Purpose

One way to analyze electrochemical signals is the wavelet transform, which transforms a signal into another representation whereby the signal information is presented in a multi‐scale manner. Using the inverse wavelet transform, it is also possible to split a signal into different components of different frequency intervals. The inverse wavelet transform is the concept underpinning this paper, the aim of which is to demonstrate that high‐frequency variations in current signals are as valuable as low‐frequency variations.

Design/methodology/approach

The set‐up for the experiments carried out consisted of two identical carbon steel working electrodes exposed to simulated concrete pore solution, sparged simultaneously with SO2 and CO2. The corresponding electrochemical current signal was studied using wavelet transform.

Findings

High‐frequency components of current signals are as informative as low‐frequency components. High‐frequency variations could show some electrochemical activities that are not obvious in the other parts.

Originality/value

This paper shows that high‐frequency variations can be taken into consideration along with low‐frequency variations, since both can provide complementary information about electrochemical activities.
Effect of the relative velocity between ship hull and seawater on the performance of sacrificial cathodic protection
Authors: Sedahmed G.H. , Farag H.A. , Hassan M.A. , Hassan I.
Published: March 2010

Purpose

The purpose of this paper is to study the effect of the relative velocity between ship hull and seawater on the rate of zinc consumption and degree of cathodic protection during sacrificial cathodic protection of steel hulls using zinc anodes.

Design/methodology/approach

The rate of zinc consumption under different relative velocities was determined by the loss in weight technique while the degree of cathodic protection of the ship hull at different distances from the anode was determined by measuring the cathode potential of the hull cathode against a silver/silver chloride reference electrode.

Findings

Within the present range of conditions, the rate of zinc consumption (R) was found to increase with increasing the relative velocity according to equations: R=3.9×10−4 Re0.0126; for Re<3,500, and R=7.36×10−6 Re0.5; for Re>3,500, where Re is the Reynolds number. The degree of cathodic protection represented by the hull (cathode) potential at a given distance from the anode was found to decrease slightly with increasing the relative velocity.

Originality/value

The present results would make it possible for the designer of sacrificial cathodic protection systems to assess the amount of zinc required to protect the ship hull under certain operating conditions more accurately than the situation where the effect of the relative velocity was not considered.
On the prevalence and scientific impact of duplicate publications in different scientific fields (1980‐2007)
Authors: Larivière Vincent , Gingras Yves
Published: March 2010

Purpose

The issue of duplicate publications has received a lot of attention in the medical literature, but much less in the information science community. This paper aims to analyze the prevalence and scientific impact of duplicate publications across all fields of research between 1980 and 2007.

Design/methodology/approach

The approach is a bibliometric analysis of duplicate papers based on their metadata. Duplicate papers are defined as papers published in two different journals having: the exact same title; the same first author; and the same number of cited references.

Findings

In all fields combined, the prevalence of duplicates is one out of 2,000 papers, but is higher in the natural and medical sciences than in the social sciences and humanities. A very high proportion (>85 percent) of these papers are published the same year or one year apart, which suggest that most duplicate papers were submitted simultaneously. Furthermore, duplicate papers are generally published in journals with impact factors below the average of their field and obtain lower citations.

Originality/value

The paper provides clear evidence that the prevalence of duplicate papers is low and, more importantly, that the scientific impact of such papers is below average.
From digital libraries to digital preservation research: the importance of users and context
Authors: Chowdhury Gobinda
Published: March 2010

Purpose

The purpose of this paper is to point out the commonalities of research in digital libraries and digital preservation with regard to the issues of users and context of information.

Design/methodology/approach

The paper's approach is a review of selected literature and reports of research projects focusing particularly on digital preservation research.

Findings

It is noted that just like the digital library community the digital preservation research community is also confronted with the challenges of capturing, storing and making use of the information related to users and context.

Practical implications

The paper points out some current research in digital preservation that aims to handle the users and context information for building future digital preservation systems. It highlights some major challenges in these areas.

Originality/value

The paper reports on the state of the art research in digital preservation.
The connection between purposive information seeking and information encountering
Authors: Pálsdóttir Ágústa
Published: March 2010

Purpose

This paper aims to explore health and lifestyle information seeking behaviour by examining the connection between purposive information seeking and information encountering.

Design/methodology/approach

Data on purposive seeking and information encountering, gathered from postal surveys in 2002 and 2007, were compared. Random samples of 1,000 Icelanders, aged 18 to 80 were used. The response rate was 51 per cent in 2002 and 47 per cent in 2007. Based on the purposive seeking in 22 sources, k‐means cluster analysis was used to draw four clusters of participants: passive, moderately passive, moderately active and active.

Findings

The results from 2007 and 2002 revealed the same kind of information seeking. The findings indicate that information encountering is an integral feature of information seeking behaviour. Information is encountered more often than sought on purpose by all clusters. Clusters that were active in purposive information seeking were also active in information encountering and those who were passive in either of the two styles of information seeking were also passive in the other.

Research limitations/implications

The response rates are considered satisfactory in postal surveys. Nevertheless, when missing data in the cluster analysis are also considered it raises a question about the validity of the findings. The findings of the studies, however, are strengthened by the fact that respondents reflect the population fairly well.

Practical implications

Improved knowledge of information seeking and how different groups within society can be reached more effectively is important for health promotion and public health practice.

Originality/value

The paper uses quantitative methods to examine the connection between purposive information seeking and information encountering.
Framing information literacy as information practice: site ontology and practice theory
Authors: Lloyd Annemaree
Published: March 2010

Purpose

Information literacy is a rich and complex social information practice that is constructed according to specific practical understandings, rules and teleoaffective features which characterise a social site or setting. This paper aims to explore the philosophical and theoretical perspective of practice theory, in particular, the ontological work of Schatzki. These perspectives are to be used to frame an understanding of the features of information literacy as sociocultural practice.

Design/methodology/approach

A theoretical perspective is introduced to examine the concept of information literacy practice by framing this analysis through a site ontology developed by Schatzki. Sociocultural and practice theory are employed in this exploration of information literacy as sociocultural practice and provide a framework for architecture of information literacy practice.

Findings

Information literacy can be understood as a critical information practice which is organised and arranged through the site of the social, rather than as a reified and decontexualised set of skills.

Research limitations/implications

Framing information literacy research through site ontology and the use of a practice perspective has implications for further research into information literacy and for the development of pedagogic practices related to information literacy instruction

Originality/value

The paper offers an alternate way of framing information literacy by introducing the concepts related to practice theory.
A tight reign
Authors: Clardy Alan , Beadle Scott
Published: March 2010

Purpose

The purpose of this paper is is to depict an example of an abusive, bullying manager; suggest what effects those abusive practices were having on individuals and the organization; note the potential ethical, legal and organizational issues involved; prompt analysis of organizational conditions and practices that allow such behavior; and promote consideration of preventive policies, programs and practices.

Design/methodology/approach

This paper is a case study based on interviews, observations and document analysis. An extended literature review was examined to prepare a companion Instructor's Manual.

Findings

The bullying and abusive behavior of a firm's senior executive was seriously damaging the value and operating performance of the firm. The training manager was in a position to promote effective organizational responses to the bullying executive.

Practical implications

A variety of administrative, legal and/or ethical requirements indicate that the training director should act. In the companion Instructor's Manual, a number of preventive and recuperative interventions are suggested.

Originality/value

This paper provides one of the first detailed case histories of the nature of bullying behavior at an executive level and the effects such behavior has on the organization.
Communicative interaction as an instrument for integration and coordination in an aerospace supply chain
Authors: Rose‐Anderssen Christen , Baldwin James , Ridgway Keith
Published: March 2010

Purpose

This paper seeks to explore the effects of communicative interaction on integration and coordination of a commercial aerospace supply chain.

Design/methodology/approach

A perspective of supply chains as complex activity networks is used for data analysis based on in‐depth interviews in a global setting. Themes for interviews were identified through literature research.

Findings

The paper finds that integration through risk‐sharing partnerships is chosen for co‐developing expertise and innovative capacity. Practices of integration and coordination through communicative interaction are emerging while they are producing innovative solutions and competitive advantage. The multi‐voiced interaction between partners in the supply chain is assisting in moving the product beyond what the airframe manufacturer could have created alone.

Originality/value

The paper provides evidence of changing interactive practices in commercial aerospace supply chains. By applying concepts of supply chains as he interaction of multiple work activities this assists in comprehending the forces of change. Communicative interaction within the supply chain is used for co‐construction of meaning to enhance change and development.
Paradexity: the convergence of paradox and complexity
Authors: Howard Anthony
Published: March 2010

Purpose

The aim of this paper is to propose a theory about the convergence of paradox and complexity and the consequences of this.

Design/methodology/approach

The author conducts an ongoing series of conversations with a range of thinkers in the academic and commercial domains

Findings

The paper finds that paradox and complexity are merging into “paradexity”. This can be observed in technological advancements that depersonalise, saturate, accelerate, and fragment the world we experience. It is contributing to the emergence of a new set of paradigms – the emotional economy, sense‐making, time expansion, and communities of interest – that will require developing four core capabilities: care, wisdom, attention and conversation.

Research limitations/implications

Further rigorous testing would be required to confirm the validity of the views expressed.

Practical implications

This paper has significant implications for the way people engage with one another and the way we organise our workforces, and offers suggestions for ways individuals and society can flourish in this environment.

Originality/value

The paper recognises the convergence of paradox and complexity and the need to work within this construct, rather than eliminate or minimise either. It would be of value to senior business leaders, human resource directors, and those involved with public policy who wish to design more effective organisations and societies.
Understanding social advocacy
Authors: London Manuel
Published: March 2010

Purpose

This paper aims to examine characteristics that contribute to leaders' emergence and development as social advocates in their organizations and communities.

Design/methodology/approach

Building on theories of social problems, influence, and impression management, this paper examines how advocacy is affected by needs and situational conditions. Advocacy is the act of supporting an idea, need, person, or group. Advocates use cognitive, emotional, and behavioral strategies to influence attitudes, behaviors, and/or decisions for the benefit of individuals or to promote organizational change and/or social welfare. Social advocacy occurs within organizations in the form of corporate social responsibility, and it occurs within communities in the form of social entrepreneurship.

Findings

This theoretical paper argues that motivation of leaders of social ventures is a function of their conviction, self‐confidence, and extroversion. Advocates' beliefs about people are likely to shape their advocacy strategies, in particular, their beliefs about whether people are likely to change their attitudes and behavior, are sensitive to possible losses and gain, and respond to information about the probabilities and outcomes of actions and events. Advocate's resilience and transformational abilities (communications and political skills, knowledge of change management, and learning orientation) are predicted to influence their success.

Originality/value

The paper discusses directions for management development research and practice to promote involvement in social ventures.
Assessing the desktop manager
Authors: Lester Donald L. , Parnell John A. , Carraher Shawn
Published: March 2010

Purpose

This paper aims to present the results of an empirical study identifying desktop managers who spend all of their time engaged with the computer and the effects this has on organizations.

Design/methodology/approach

A survey was administered to 30 organizations in a southwestern US state to determine the presence of desktop managers.

Findings

The paper finds that desktop managers in an organization negatively impacted job satisfaction, organizational commitment, organizational citizenship, and the zest and vitality of subordinates.

Research limitations/implications

Only employees from 30 organizations were surveyed, and all were located in a specific geographic area of the USA.

Practical implications

The negative impact of desktop managers on organizational members points to a disturbing trend, that knowledge workers are not having their interactive communication needs with managers met.

Originality/value

The original scale developed for the study shows promise in identifying the presence of desktop managers in organizations.
Servant leadership in the People's Republic of China: a case study of the public sector
Authors: Han Yong , Kakabadse Nada K. , Kakabadse Andrew
Published: March 2010

Purpose

This paper seeks to explore whether the Western concept of servant leadership holds the same meaning in the public sector of the cross‐cultural context of China and to identify whether there is an alternative term in the Chinese language that closely relates to the concept of servant leadership

Design/methodology/approach

An inductive approach is adopted based on critical incident technique, using an open‐ended survey to collect the data.

Findings

It was found that the concept of servant leadership holds parallel meaning in China to that of the West and that the Chinese concept of servant leadership can be described precisely as public servant leadership in the public sector and servant leadership in the non‐public sector. When asked to characterize Chinese servant leadership in the public sector, the study respondents consider six types of servant leadership similar to the West but also three types of Chinese extended servant leadership.

Originality/value

The paper is a first attempt to examine servant leadership in the public sector in China. It not only reports various forms of Chinese servant leadership orientation, but also compares and contrasts various servant leadership forms between China and the West, highlighting research gaps for future research within the context of the People's Republic of China (PRC) and the West.