bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo estimation of uncertainties in BEIS3 emission outputs and their effects on uncertainties in chemical transport model predictions
Authors: Hanna S. R. , Russell A. G. , Wilkinson J. G. , Vukovich J. , Hansen D. A.
Published: January 2005

A Monte Carlo (MC) probabilistic approach is used to estimate uncertainties in the emissions outputs of the Biogenics Emission Inventory System Version 3 (BEIS3) model and subsequent ozone outputs of three Chemical Transport Models (CTMs) due to uncertainties in many key BEIS3 biogenics emissions model parameters and inputs. BEIS3 was developed by the Environmental Protection Agency to estimate emissions of biogenic substances such as isoprene, monoterpenes, oxygenated and other volatile organic compounds (OVOCs), and biogenic nitric oxide (BNO). Uncertainties are investigated for three time periods, 24–29 May, 11–15 July, and 4–9 September 1995, which are ozone episodes that have been extensively studied by others as part of emissions control planning exercises. In the MC approach, 1000 samples are drawn randomly and independently from seventeen BEIS3 parameters and inputs, whose distribution shapes and variances are determined from literature reviews. The 95% confidence range on the calculated uncertainties in isoprene and BNO emissions cover approximately an order of magnitude. On the other hand, the 95% confidence ranges on the calculated uncertainties in monoterpenes and OVOC emissions are much smaller: about ±20%. Correlations are calculated between the 1000 MC samples of pairs of variations in model parameters or inputs and variations in BEIS3 daily emissions estimates for individual grid squares. A few significant correlations are found for some of the assumed model parameters. The MC uncertainties in the CTM‐predicted 1‐ and 8‐hour averaged ozone concentrations were studied by drawing 20 random samples from the 1000 sets of BEIS3 outputs and running each CTM (MAQSIP, UAM‐V, and URM) 20 times for the three episodes. The estimated total uncertainties of ±15 to 20% are found to be nearly the same for the three CTMs over the three time periods, for 1‐ and 8‐hour averages.
Comparison of the measured and simulated isoprene nitrate distributions above a forest canopy
Authors: Giacopelli P. , Ford K. , Espada C. , Shepson P. B.
Published: January 2005

It is known that isoprene nitrate production can represent a significant sink for atmospheric NOx and free radicals, and therefore this chemistry is important to understanding tropospheric O3 and the fate of NOx in forest‐impacted environments. Although six structural isoprene nitrate isomers can be produced from OH reaction with isoprene in the presence of NO, these have not been separately quantified in the atmosphere. A zero‐dimensional isoprene photochemistry model was developed based on the known gas‐phase isoprene oxidation chemistry for comparison with isoprene nitrate ambient concentration data obtained from field and laboratory measurements. The model incorporates calculated individual branching ratios for each isomer as well as rate constants for the reaction of each isomeric nitrate with the OH radical and O3 and losses from the boundary layer by dry deposition and vertical mixing. The model indicates that under atmospheric conditions, there should be three nitrate isomers that represent 86% of the total, while our ambient measurements indicate only two dominant nitrate isomers. This contrasts significantly with what is observed in the laboratory because of atmospheric conversion to other nitrogen‐containing products. These secondary nitrates are likely to be a significant fraction of NOy in forest environments.
On the monotonicity of scalar curvature in classical and quantum information geometry
Authors: Gibilisco Paolo , Isola Tommaso
Published: January 2005

We study the monotonicity under mixing of the scalar curvature for the α-geometries on the simplex of probability vectors. From the results obtained and from numerical data, we are led to some conjectures about quantum α-geometries and Wigner–Yanase–Dyson information. Finally, we show that this last conjecture implies the truth of the Petz conjecture about the monotonicity of the scalar curvature of the Bogoliubov–Kubo–Mori monotone metric.
Fast centroid molecular dynamics: A force-matching approach for the predetermination of the effective centroid forces
Authors: Hone Tyler D. , Izvekov Sergei , Voth Gregory A.
Published: January 2005

A fast centroid molecular dynamics (CMD) methodology is proposed in which the effective centroid forces are predetermined through a force-matching algorithm applied to a standard path integral molecular dynamics simulation. The resulting method greatly reduces the computational cost of generating centroid trajectories, thus extending the applicability of CMD. The method is applied to the study of liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The static and dynamical results are compared to those obtained from full adiabatic CMD simulations and found to be in excellent agreement for all three systems; the transport properties are also compared to experiment and found to have a similar level of agreement.
Influence of impurities on the uniform atmospheric-pressure discharge in helium
Authors: Wang Yanhui , Wang Dezhen
Published: January 2005

The influence of small nitrogen impurities on the uniform barrier discharge at atmospheric pressure in helium is investigated by numerical simulation with a one-dimensional fluid model. The simulation results show that in different discharge modes the influence of impurities is completely different. For glow discharge, small impurities result in the breakdown voltage dropping and thus cause the decrease in charged particle densities and discharge current density. In the case of Townsend discharge, nitrogen impurities can lead to the increase of charged particle densities and discharge current density, and even the change of discharge mode, but do not have a distinct impact on the breakdown voltage.
Photoelectron anisotropy and channel branching ratios in the detachment of solvated iodide cluster anions
Authors: Mabbs Richard , Surber Eric , Sanov Andrei
Published: January 2005

Photoelectron spectra and angular distributions in 267 nm detachment of the I−⋅Ar, I−⋅H2O, I−⋅CH3I, and I−⋅CH3CN cluster anions are examined in comparison with bare I− using velocity-map photoelectron imaging. In all cases, features are observed that correlate to two channels producing either I(2P3/2) or I(2P1/2). In the photodetachment of I− and I−⋅Ar, the branching ratios of the P1/22 and P3/22 channels are observed to be ≈0.4, in both cases falling short of the statistical ratio of 0.5. For I−⋅H2O and I−⋅CH3I, the P1/22 to P3/22 branching ratios are greater by a factor of 1.6 compared to the bare iodide case. The relative enhancement of the P1/22 channel is attributed to dipole effects on the final-state continuum wave function in the presence of polar solvents. For I−⋅CH3CN the P1/22 to P3/22 ratio falls again, most likely due to the proximity of the detachment threshold in the excited spin-orbit channel. The photoelectron angular distributions in the photodetachment of I−, I−⋅Ar, I−⋅H2O, and I−⋅CH3CN are understood within the framework of direct detachment from I−. Hence, the corresponding anisotropy parameters are modeled using variants of the Cooper-Zare central-potential model for atomic-anion photodetachment. In contrast, I−⋅CH3I yields nearly isotropic photoelectron angular distributions in both detachment channels. The implications of this anomalous behavior are discussed with reference to alternative mechanisms, affording the solvent molecule an active role in the electron ejection process.
Directing oncogenic fusion genes into stem cells via an
SCL
enhancer
Authors: Eguchi Mariko , Eguchi-Ishimae Minenori , Green Anthony , Enver Tariq , Greaves Mel
Published: January 2005

TEL-TRKC
is a fusion gene generated by chromosomal translocation and encodes an activated tyrosine kinase. Uniquely, it is found in both solid tumors and leukemia. However, a single exon difference (in
TEL
) in TEL-TRKC fusions is associated with the two sets of cancer phenotypes. We expressed the two
TEL-TRKC
variants
in vivo
by using the 3′ regulatory element of
SCL
that is selectively active in a subset of mesodermal cell lineages, including endothelial and hematopoietic stem cells and progenitors. The leukemia form of
TEL-TRKC
(–exon 5 of
TEL
) enhanced hematopoietic stem cell renewal and initiated leukemia. In contrast, the
TEL-TRKC
solid tumor variant (+
TEL
exon 5) elicited an embryonic lethal phenotype with impairment of both angiogenesis and hematopoiesis indicative of an effect at the level of the hemangioblasts. The ability of TEL-TRKC to repress expression of Flk1, a critical regulator of early endothelial and hematopoietic cells, depended on TEL exon 5. These data indicate that related oncogenic fusion proteins similarly expressed in a hierarchy of early stem cells can have selective, cell type-specific developmental impacts.
DNA damage-induced mitotic catastrophe is mediated by the Chk1-dependent mitotic exit DNA damage checkpoint
Authors: Huang Xingxu , Tran Thanh , Zhang Lingna , Hatcher Rashieda , Zhang Pumin
Published: January 2005

Mitotic catastrophe is the response of mammalian cells to mitotic DNA damage. It produces tetraploid cells with a range of different nuclear morphologies from binucleated to multimicronucleated. In response to DNA damage, checkpoints are activated to delay cell cycle progression and to coordinate repair. Cells in different cell cycle phases use different mechanisms to arrest their cell cycle progression. It has remained unclear whether the termination of mitosis in a mitotic catastrophe is regulated by DNA damage checkpoints. Here, we report the presence of a mitotic exit DNA damage checkpoint in mammalian cells. This checkpoint delays mitotic exit and prevents cytokinesis and, thereby, is responsible for mitotic catastrophe. The DNA damage-induced mitotic exit delay correlates with the inhibition of Cdh1 activation and the attenuated degradation of cyclin B1. We demonstrate that the checkpoint is Chk1-dependent.
Preparation of rhodamine-labelled tubulin and its reassembly in guard cells in leaves of Vicia faba L.
Authors: Rong Yu , Ming Yuan , Xue-Chen Wang
Published: January 2005

Tubulin from fresh pig brain was extracted through two cycles of polymerization and depolymerization, purified by chromatography on an ion-exchange column and labelled with 5(6)-carboxytetramethylrhodamine succinimidyl ester. We prepared 10.8 mg/ml rhodamine-labelled tubulin probe (dye/protein=0.6) and then microinjected it into living guard cells in leaves of Vicia faba L. After 5–10 min, a network of microtubules (MTs) could clearly be observed in the guard cells under a confocal laser scanning microscope. In opening guard cells, the cortical MTs radiated from the ventral wall to the dorsal wall and in closed guard cells the radial MTs were completely depolymerized into random and diffuse fragments. This shows that pig brain tubulin can easily be incorporated into MTs in guard cells, and that the dynamic behaviour of MTs can be examined directly in vivo during stomatal movement.
Factors influencing the efficiency of isolation and culture of human embryonic germ cells
Authors: Jin-Lian Hua , Zhong-Ying Dou , Xiao-Ming Xu , Song Li , Yu-Ai Yang , An-Min Lei
Published: January 2005

Embryonic germ (EG) cells are pluripotent cells derived from the primordial germ cells of gonads, gonadal ridges and mesenteries, and analogies of foetuses, with the ability to undergo both self-renewal and multiple differentiation. These cells can differentiate into derivatives of all three embryonic germ layers when transferred to anin vitroenvironment and have the ability to form any fully differentiated cell of the body. The present paper investigates some factors influencing the efficiency of isolation and culture of human EG cells, such as foetus age, culture serum, added cytokines and feeder cells. The results demonstrate that foetuses of 7–12 weeks are optimal forin vitroculture of human EG cells. The basic medium consisted of DMEM, 1×non-essential amino acids, 2 mM l-glutamine and 1 mM sodium pyruvate. Supplementation with 15% foetal bovine serum, 4 ng/ml human recombinant leukaemia inhibitory factor, 4 ng/ml basic fibroblast growth factor and 20 ng/ml stem cell factor clearly improved the efficiency of isolation and culture of human EG cells. Murine embryonic fibroblasts were better feeder cells than human embryonic fibroblasts, bovine embryonic fibroblasts or STO cell line.
Strictly positive definite functions on the unit circle
Authors: Sun Xingping
Published: January 2005

We study strictly positive definite functions on the unit circle in the Euclidean space of dimension two. We develop several conditions pertaining to the determination of such functions. The major result is obtained by considering the set of real numbers as a vector space over the field of rational numbers and then applying the Kronecker approximation theorem and Weyl’s criterion on equidistributions.
Some properties of the gamma and psi functions, with applications
Authors: Qiu S.-L. , Vuorinen M.
Published: January 2005

In this paper, some monotoneity and concavity properties of the gamma, beta and psi functions are obtained, from which several asymptotically sharp inequalities follow. Applying these properties, the authors improve some well-known results for the volume

Ω
n

\Omega _n

of the unit ball

B
n

⊂

R

n

B^n\subset \mathbb {R}^n

, the surface area

ω

n
−
1

\omega _{n-1}

of the unit sphere

S

n
−
1

S^{n-1}

, and some related constants.
Trivariate spline approximations of 3D Navier-Stokes equations
Authors: Awanou Gerard , Lai Ming-Jun
Published: January 2005

We present numerical approximations of the 3D steady state Navier-Stokes equations in velocity-pressure formulation using trivariate splines of arbitrary degree

d
d

and arbitrary smoothness

r
r

with

r
>
d

r>d

. Using functional arguments, we derive the discrete Navier-Stokes equations in terms of

B
B

-coefficients of trivariate splines over a tetrahedral partition of any given polygonal domain. Smoothness conditions, boundary conditions and the divergence-free condition are enforced through Lagrange multipliers. The pressure is computed by solving a Poisson equation with Neumann boundary conditions. We have implemented this approach in MATLAB and present numerical evidence of the convergence rate as well as experiments on the lid driven cavity flow problem.
Algorithms without accuracy saturation for evolution equations in Hilbert and Banach spaces
Authors: Gavrilyuk Ivan , Makarov Volodymyr
Published: January 2005

We consider the Cauchy problem for the first and the second order differential equations in Banach and Hilbert spaces with an operator coefficientA(t)A(t)depending on the parametertt. We develop discretization methods with high parallelism level and without accuracy saturation; i.e., the accuracy adapts automatically to the smoothness of the solution. For analytical solutions the rate of convergence is exponential. These results can be viewed as a development of parallel approximations of the operator exponentiale−tAe^{-tA}and of the operator cosine familycos⁡At\cos {\sqrt {A} t}with a constant operatorAApossessing exponential accuracy and based on the Sinc-quadrature approximations of the corresponding Dunford-Cauchy integral representations of solutions or the solution operators.
𝑝-class groups of certain extensions of degree 𝑝
Authors: Wittmann Christian
Published: January 2005

Let

p
p

be an odd prime number. In this article we study the distribution of

p
p

-class groups of cyclic number fields of degree

p
p

, and of cyclic extensions of degree

p
p

of an imaginary quadratic field whose class number is coprime to

p
p

. We formulate a heuristic principle predicting the distribution of the

p
p

-class groups as Galois modules, which is analogous to the Cohen-Lenstra heuristics concerning the prime-to-

p
p

-part of the class group, although in our case we have to fix the number of primes that ramify in the extensions considered. Using results of Gerth we are able to prove part of this conjecture. Furthermore, we present some numerical evidence for the conjecture.
Lactobacillus delbrueckii subsp. indicus subsp. nov., isolated from Indian dairy products
Authors: Dellaglio Franco , Felis Giovanna E. , Castioni Anna , Torriani Sandra , Germond Jacques-Edouard
Published: January 2005

Four strains isolated from Indian dairy products and initially identified as Lactobacillus delbrueckii could not be assigned to a definite subspecies because molecular identification and phenotypic traits did not agree with those of recognized subspecies of L. delbrueckii. Hybridization of total DNA (78–86 % against type strains of the other three subspecies), AFLP and RAPD-PCR fingerprints, phylogenetic analysis based on 16S rRNA gene sequences and sequence analysis of two coding genes (recA and hsp60), together with phenotypic profiles, indicated that the four strains form a coherent cluster and represent a novel subspecies, for which the name Lactobacillus delbrueckii subsp. indicus subsp. nov. is proposed. The type strain is NCC725T (=LMG 22083T=DSM 15996T).
Streptomyces koyangensis sp. nov., a novel actinomycete that produces 4-phenyl-3-butenoic acid
Authors: Lee Jee Yeon , Lee Jung Yeop , Jung Ho Won , Hwang Byung Kook
Published: January 2005

A 4-phenyl-3-butenoic acid-producing actinomycete, designated strain VK-A60T, was isolated from a soil sample collected from Koyang, Korea. Morphological and chemical characteristics of the strain were consistent with those of the genus Streptomyces. The cell wall of the strain contains ll-diaminopimelic acid. The predominant fatty acids are anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The strain formed a distinct monophyletic line within the 16S rRNA gene sequence phylogenetic tree. Analyses of its morphological, physiological and biochemical characteristics, together with random amplified polymorphic DNA and DNA–DNA relatedness data, confirmed that strain VK-A60T represents a novel Streptomyces taxon that is distinguishable from closely related reference strains. Strain VK-A60T (=KCCM 10555T=NBRC 100598T) is proposed as the type strain of a novel species, for which the name Streptomyces koyangensis sp. nov. is proposed.
Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.
Authors: Jurado Valme , Groth Ingrid , Gonzalez Juan M. , Laiz Leonila , Saiz-Jimenez Cesareo
Published: January 2005

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).
On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes
Authors: Harper James T. , Waanders Esmé , Keeling Patrick J.
Published: January 2005

A global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or ‘supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for much of the phylogenies is decreased over previous analyses that concatenated fewer genes for fewer taxa. Nevertheless, four of the six chromalveolate lineages (apicomplexans, ciliates, dinoflagellates and heterokonts) consistently form a monophyletic assemblage, whereas the remaining two (cryptomonads and haptophytes) form a weakly supported group. Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms.
Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest
Authors: Thawai Chitti , Tanasupawat Somboon , Itoh Takashi , Suwanborirux Khanit , Suzuki Ken-ichiro , Kudo Takuji
Published: January 2005

Two actinomycete strains, LK2-10T and LK2-5, which produced single, non-motile spores, were isolated from peat swamp forest soil in Yala Province, Thailand. A polyphasic study was carried out to establish the taxonomic position of these strains. Morphological and chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora. Phylogenetic analysis using 16S rRNA gene sequences also indicated that these strains should be classified in the genus Micromonospora and clearly separated from their closest relative, Micromonospora nigra DSM 43818T. Furthermore, a combination of DNA–DNA hybridization results and physiological and biochemical properties indicated that these strains were distinguished from all recognized Micromonospora species. These strains therefore represent a novel species, for which the name Micromonospora eburnea sp. nov. is proposed. The type strain is LK2-10T (=JCM 12345T=PCU 238T=DSM 44814T=TISTR 1531T).
Microbacterium halotolerans sp. nov., isolated from a saline soil in the west of China
Authors: Li Wen-Jun , Chen Hua-Hong , Kim Chang-Jin , Park Dong-Jin , Tang Shu-Kun , Lee Jae-Chan , Xu Li-Hua , Jiang Cheng-Lin
Published: January 2005

A Gram-positive short rod isolated from a saline soil in China was characterized using a polyphasic approach. This actinobacterium grew over a wide salinity range [0–15 % NaCl, 0–20 % KCl and 0–30 % MgCl2.6H2O (w/v); optimum concentrations for growth were 5 % NaCl, 5–10 % KCl, 10 % MgCl2.6H2O]. The optimum growth temperature and pH were 28–30 °C and 7·0–8·0, respectively. Chemotaxonomic features (peptidoglycan-type B2β with glycolyl residues; major menaquinones MK-10 and MK-11; predominating iso- and anteiso-branched cellular fatty acids; DNA G+C content 66·5 mol%) placed this organism within the genus Microbacterium. 16S rRNA gene sequence analysis confirmed this classification of the strain, but showed that it was distinct from its nearest neighbours. It formed a separate branch with type strains of the genus Microbacterium, and also shared low sequence similarity with them (<96 %). Based on phenotypic and molecular taxonomic results, it is proposed that the unknown isolate should be classified as a novel species in the genus Microbacterium, for which the name Microbacterium halotolerans sp. nov. is proposed. The type strain is YIM 70130T (=KCTC 19017T=CIP 108071T).
Lactobacillus satsumensis sp. nov., isolated from mashes of shochu, a traditional Japanese distilled spirit made from fermented rice and other starchy materials
Authors: Endo Akihito , Okada Sanae
Published: January 2005

Gram-positive, rod-shaped, motile lactic acid bacteria (strains NRIC 0603, NRIC 0604T, NRIC 0605 and NRIC 0606) were isolated from shochu mashes using an enrichment culture approach. These strains clustered in the Lactobacillus casei–Pediococcus group and were closely related to Lactobacillus nagelii and Lactobacillus mali on the basis of 16S rRNA gene sequence similarity. Levels of DNA–DNA relatedness revealed genotypic separation of the four isolates from the above two species. The isolates are therefore considered to represent a novel species, for which the name Lactobacillus satsumensis is proposed. The type strain is NRIC 0604T (=JCM 12392T=DSM 16230T).
Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters
Authors: Ma Kai , Liu Xiaoli , Dong Xiuzhu
Published: January 2005

Two methanogenic strains, 8-2T and 4-1, with rod-shaped (0·4–0·5×3–5 μm), non-motile cells, sometimes observed in chains, were isolated from two anaerobic digesters in Beijing, China. The two strains used H2/CO2 and formate for growth and produced methane. The temperature range for growth was 25–50 °C, with fastest growth at 37 °C. The pH ranges for growth and methane production were 6·5–8·0 for strain 8-2T and 6·8–8·6 for strain 4-1, with the fastest growth at pH 7·2 for strain 8-2T and pH 7·5–7·7 for strain 4-1. The G+C content of genomic DNA for strain 8-2T was 38·9 mol%. The similarity levels of the 16S rRNA sequence of strain 8-2T with other species of the genus Methanobacterium ranged from 93·8 to 96·0 %. Based on the phylogenetic analysis and phenotypic characteristics, the novel species Methanobacterium beijingense sp. nov. is proposed, with the type strain 8-2T (=DSM 15999T=CGMCC 1.5011T).
Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria)
Authors: Rajaniemi Pirjo , Hrouzek Pavel , Kaštovská Klára , Willame Raphaël , Rantala Anne , Hoffmann Lucien , Komárek Jiří , Sivonen Kaarina
Published: January 2005

The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.
‘Candidatus Phytoplasma pini’, a novel taxon from Pinus silvestris and Pinus halepensis
Authors: Schneider Bernd , Torres Ester , Martín María P. , Schröder Manfred , Behnke Heinz-Dietmar , Seemüller Erich
Published: January 2005

Pinus silvestris and Pinus halepensis trees grown in Germany and Spain, respectively, showing abnormal shoot branching, dwarfed needles and other symptoms were examined for the presence of plant-pathogenic mollicutes (phytoplasmas). While phytoplasmas could not be detected unambiguously with microscopical methods, PCR amplification using universal phytoplasma primers yielded positive results. Samples collected from symptomatic and non-symptomatic plant parts of both symptomatic Pinus silvestris and Pinus halepensis trees tested positive. Also, surrounding non-symptomatic trees proved to be phytoplasma-infected. Comparisons revealed that the 16S rRNA gene sequences of the phytoplasmas identified in Pinus silvestris and Pinus halepensis were nearly identical. However, the pine phytoplasma is only distantly related to other phytoplasmas. The closest relatives are members of the palm lethal yellowing and rice yellow dwarf groups and ‘Candidatus Phytoplasma castaneae’, which share between 94·5 and 96·6 % 16S rRNA gene sequence similarity. From these data it can be concluded that the phytoplasmas identified in the two Pinus species represent a coherent but discrete taxon; it is proposed that this taxon be distinguished at putative species level under the name ‘Candidatus Phytoplasma pini’.
Bacillus saliphilus sp. nov., isolated from a mineral pool in Campania, Italy
Authors: Romano Ida , Lama Licia , Nicolaus Barbara , Gambacorta Agata , Giordano Assunta
Published: January 2005

A haloalkaliphilic Gram-positive bacterium, strain 6AGT, that grew aerobically at an optimum temperature of 37 °C and at pH 7–10 (optimum 9·0), was isolated from algal mat from a mineral pool located in Malvizza in the Campania region (southern Italy). The isolate tolerated high concentrations of NaCl, up to 25 %. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Bacillus. Analysis of the 16S rRNA gene sequence revealed high similarity between strain 6AGT and an unidentified isolate from Hailaer soda lake (China) (99·9 % identity) and two Kenyan isolates, 3E1 and WE4 (98·3 and 97·8 % identity, respectively). The G+C content of the DNA was 48·4 mol%. The predominant respiratory quinones were MK-7(H2), MK-7(H4) and DMK-7(H2); phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. iC15 : 0 and aiC15 : 0 were the major fatty acids. Strain 6AGT accumulated osmolytes. The phylogenetic distance of strain 6AGT (=DSM 15402T=ATCC BAA-957T) from any recognized species within the genus Bacillus allowed it to be classified as the type strain of Bacillus saliphilus sp. nov.
Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lysenko Anatoly M. , Frolova Galina M. , Mikhailov Valery V. , Bae Kyung Sook , Lee Dong Hyuck , Kim In Seop
Published: January 2005

A novel marine bacterium, strain KMM 6050T, was isolated from the sea urchin Strongylocentrotus intermedius, which inhabits the Sea of Japan. The strain studied was strictly aerobic, heterotrophic, yellow–orange-pigmented, motile by gliding, Gram-negative and oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive. The results of 16S rRNA gene sequence analysis showed that strain KMM 6050T occupies a distinct lineage within the family Flavobacteriaceae and is most closely related to the species Mesonia algae and Salegentibacter salegens (sequence similarity of 92·5–92·6 %). The DNA G+C content of KMM 6050T was 39·6 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were i15 : 0, a15 : 0, 15 : 0, i16 : 1, i16 : 0, i16 : 0 3-OH and i17 : 0 3-OH. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium has been assigned to the genus Gramella gen. nov., as Gramella echinicola sp. nov. The type strain is KMM 6050T (=KCTC 12278T=NBRC 100593T=LMG 22585T).
Sporidiobolus longiusculus sp. nov. and Sporobolomyces patagonicus sp. nov., novel yeasts of the Sporidiobolales isolated from aquatic environments in Patagonia, Argentina
Authors: Libkind Diego , Gadanho Mário , van Broock Maria , Sampaio José Paulo
Published: January 2005

During a survey of carotenogenic yeasts carried out in north-western Patagonia (Argentina), several ballistoconidia-producing strains belonging to the order Sporidiobolales were isolated from aquatic environments. Five strains were found to represent two novel species, for which the names Sporidiobolus longiusculus and Sporobolomyces patagonicus are proposed, with CBS 9654T (=PYCC 5818T=CRUB 1044T) and CBS 9657T (=PYCC 5817T=CRUB 1038T) as the type strains, respectively. The elongated basidia, which are five to six times longer that those of the remaining species of the genus Sporidiobolus, are a particular micromorphological feature of Sporidiobolus longiusculus. On the basis of the sequences of the D1/D2 domains of the 26S rRNA gene, the species most closely related to Sporidiobolus longiusculus is Sporobolomyces bannaensis, whereas Sporobolomyces marcillae is the closest relative of Sporobolomyces patagonicus. Complete internal transcribed spacer sequence analysis confirmed the separate position of Sporidiobolus longiusculus, whereas for Sporobolomyces patagonicus no nucleotide differences were found with respect to Sporidiobolus pararoseus CBS 491T. Negative mating experiments between strains of Sporobolomyces patagonicus and strains of Sporidiobolus pararoseus together with the low DNA–DNA reassociation values for the type strains of the two species validated the proposal of Sporobolomyces patagonicus as a distinct species. Information on additional Patagonian Sporobolomyces isolates is also included in this report.
Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’, isolated from the green alga Ulva fenestrata
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lee Dong Hyuck , Lysenko Anatoly M. , Shevchenko Lyudmila S. , Frolova Galina M. , Mikhailov Valery V. , Lee Kang Hyun , Bae Kyung Sook
Published: January 2005

The taxonomic position of a novel marine bacterium isolated from the green alga Ulva fenestrata collected in the Sea of Japan was established. Cells of the strain studied, designated KMM 6017T, were strictly aerobic, heterotrophic, pink-pigmented, non-motile by gliding, Gram-negative and oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive. 16S rRNA gene sequence analysis indicated that the strain occupied a distinct lineage within the phylum ‘Bacteroidetes’ and formed a cluster with [Flexibacter] tractuosus and Reichenbachia agariperforans. The G+C content of the DNA of KMM 6017T was 40·2 mol%. The major respiratory quinone was MK-7. The predominant fatty acids were i15 : 1, i15 : 0 and i17 : 0 3-OH (34·2, 24 and 7·7 %, respectively). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium was assigned to the genus Roseivirga gen. nov., as Roseivirga ehrenbergii gen. nov., sp. nov. The type strain is KMM 6017T (=KCTC 12282T=LMG 22567T).
The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77
Authors:   Judicial Commission of the International Committee on Systematics of Prokaryotes
Published: January 2005

The Judicial Commission of the International Committee for Systematics of Prokaryotes decided that the type species of the genus Paenibacillus is Paenibacillus polymyxa.
Knowledge‐based design aid tool for power electronic converters
Authors: Omrane Bouketir , Mariun Norman , Aris Ishak , Mahmoud Senan , Soib Taib
Published: January 2005

Purpose

The paper aims to develop a CAD tool power electronics converters.

Design/methodology/approach

Integration of knowledge base techniques with OOP paradigm. Using Visual Basis class builder, 15 classes were built to form the kernel of the tool's KB.

Findings

A knowledge‐based CAD tool was developed to ease the design of power electronics converters. It can be considered a learning aid tool too.

Research limitations/implications

The knowledge base of developed tool can be expanded to accommodate large number of topologies. The GUI can be also ameliorated to a better look and interaction process.

Practical implications

With proper enhancements, the purpose of the developed tool can be upgraded from educational one to industrial one.

Originality/value

Beside the methodology, the new thing in the paper is the specificity of the application of the tool (i.e. in power electronics).
Transformation of geometric models into orthogonal polyhedra using fuzzy logic
Authors: Obiała R. , Topping B.H.V. , Seed G.M. , Clark D.E.R.
Published: January 2005

Purpose

This paper describes how non‐orthogonal geometric models may be transformed into orthogonal polyhedral models. The main purpose of the transformation is to obtain a geometric model that is easy to describe and further modify without loss of topological information from the original model.

Design/methodology/approach

The transformation method presented in this paper is based on fuzzy logic (FL). The idea of using FL for this type of transformation was first described by Takahashi and Shimizu. This paper describes both philosophy and techniques behind the transformation method as well as its application to some example 2D and 3D models. The problem in this paper is to define a transformation technique that will change a non‐orthogonal model into a similar orthogonal model. The orthogonal model is unknown at the start of the transformation and will only be specified once the transformation is complete. The model has to satisfy certain conditions, i.e. it should be orthogonal.

Findings

The group of non‐orthogonal models that contain triangular faces such as tetrahedra or pyramids cannot be successfully recognized using this method. This algorithm fails to transform these types of problem because to do so requires modification of the structure of the model. It appears that only when the edges are divided into pieces and the sharp angles are smoothed then the method can be successfully applied. Even though the method cannot be applied to all geometric models many successful examples for 2D and 3D transformation are presented. Orthogonal models with the same topology, which make them easier to describe, are obtained.

Originality/value

This transformation makes it possible to apply simple algorithms to orthogonal models enabling the solution of complex problems usually requiring non‐orthogonal models and more complex algorithms.
Numerical formulation for solving soil/tool interaction problem involving large deformation
Authors: Renon Nicolas , Montmitonnet Pierre , Laborde Patrick
Published: January 2005

Purpose – The aim of this work is to provide a global 3D finite element (FE) model devoted to the modelling of superficial soil ploughing in the large deformation range and for a vast class of soil treatment tools. Design/methodology/approach – We introduced soil constitutive equation in a FE software initially designed for the metal forming. We performed the numerical integration of the non‐linear ploughing problem. Non‐linearities encountered by the problem can be summed up: as soil constitutive equation (idealized with non‐associated compressible plastic law), unilateral frictional contact conditions (with a rigid body), geometrical non‐linearities (the ploughing tool) and large deformation range. To handle such difficulties we performed several numerical methods as implicit temporal scheme, Newton‐Raphson, non‐symmetric iterative solver, as well as proper approximation on stress and strain measures. Findings – Main results deal with the validation of the integration of the non‐linear constitutive equation in the code and a parametric study of the ploughing process. The influence of tool geometric parameters on the soil deformation modes and on the force experienced on the tools had been point out. As well, the influence of soil characteristics as compressibility had been analyzed. Research limitations/implications – This research is devoted to perform a numerical model applicable for a large range of soil treatment tools and for a large class of soil. However, taking into account all kind of soil is utopist. So limitations met are essentially related to the limit of the accuracy of the elasto‐plastic idealization for the soil. Practical implications – In practice the numerical model exposed in the paper can clearly help to improve and optimize any process involving superficial soil submitted to the mechanical action of a rigid body. Originality/value – The original value of the paper is to provide a global and an applicable numerical model able to take into account the main topics related to the ploughing of superficial soils. Industrials in geotechnics, in agriculture or in military purposes can benefit in using such numerical model.
Reliability analysis of concrete structures with neural networks and response surfaces
Authors: Martins Gomes Herbert , Miguel Awruch Armando
Published: January 2005

Purpose

To research the feasibility in using artificial neural networks (ANN) and response surfaces (RS) techniques for reliability analysis of concrete structures.

Design/methodology/approach

The evaluation of the failure probability and safety levels of structural systems is of extreme importance in structural design, mainly when the variables are eminently random. It is necessary to quantify and compare the importance of each one of these variables in the structural safety. RS and the ANN techniques have emerged attempting to solve complex and more elaborated problems. In this work, these two techniques are presented, and comparisons are carried out using the well‐known first‐order reliability method (FORM), with non‐linear limit state functions. The reliability analysis of reinforced concrete structure problems is specially considered taking into account the spatial variability of the material properties using random fields and the inherent non‐linearity.

Findings

It was observed that direct Monte Carlo simulation technique has a low performance in complex problems. FORM, RS and neural networks techniques are suitable alternatives, despite the loss of accuracy due to approximations characterizing these methods.

Research limitations/implications

The examples tested are limited to moderated large non‐linear reinforced concrete finite element models. Conclusions are drawn based on the examples.

Practical implications

Some remarks are outlined regarding the fact that RS and ANN techniques have presented equivalent precision levels. It is observed that in problems where the computational cost of structural evaluations (computing failure probability and safety levels) is high, these two techniques could improve the performance of the structural reliability analysis through simulation techniques.

Originality/value

This paper is important in the field of reliability analysis of concrete structures specially when neural networks or RS techniques are used.
Awareness of message source and its association with the impacts of sun protection campaigns in Australia
Authors: Smith Ben J. , Bauman Adrian E. , McKenzie Jeanie , Thomas Margaret
Published: January 2005

Purpose

To examine whether awareness of the source of sun protection campaigns in New South Wales, Australia was associated with message recall and sun protection knowledge and behaviours.

Design/methodology/approach

Telephone surveys of random samples (n=800) of parents and other carers of children under 12 years of age were conducted before and after the first two campaigns and after the third campaign.

Findings

Recognition of the NSW Cancer Council (NSWCC) as the message source increased after each campaign. Cross‐sectional analyses revealed that after the first and third campaigns those who could identify the NSWCC were 1.4‐1.7 times more likely than those who could not to demonstrate knowledge about child sun protection practices (p<0.05). After the first campaign those with accurate message source awareness were 1.4 times more likely to report using sunscreen or clothing to protect their children, while after campaign three this awareness was associated with a greater likelihood (OR 1.6, p<0.05) of using hats, sunscreen and protective clothing.

Research limitations/implications

While causality cannot be determined using a cross‐sectional design, the use of serial population surveys to analyse the relationship between message source awareness and sun protection knowledge and behaviours strengthens the basis for examining the role of this factor.

Practical implications

Presenting a readily identifiable and credible message source is likely to enhance the impact of health campaigns and this factor should be given attention in the pre‐testing of communications.

Originality/value

The importance of a credible communication source has been postulated by various theorists, but this one of few studies to examine the role played this factor in a population‐wide, health promotion campaign.
The role of university libraries in supporting research in Hong Kong: facing a new challenge
Authors: Wai Fan Ka
Published: January 2005

Purpose

To discuss how Hong Kong university libraries can help young professors and PhD students publish their articles in SCI (Science Citation Index) and SSCI (Social Science Citation Index) journals.

Design/methodology/approach

With reference to the opinions of experts on how to publish work successfully, this paper provides practical advice for university libraries in Hong Kong.

Findings

After collecting the opinions of experts and browsing the web sites of many university libraries throughout the world, suggests that Hong Kong universities can offer a variety of services in supporting research. The university libraries may build up electronic resources to gather more research information and journals information for helping young professors and PhD students publish their works.

Practical implications

To provide very useful and practical advice for Hong Kong university libraries when facing the new challenge in support of research.

Originality/value

During recent years, the Hong Kong universities have been facing budget cuts from the government, and have been placed under the pressure of transforming into centers of excellence and establishing themselves among the best in the world. This paper offers practical help to Hong Kong university libraries such as how to play an active and important role in providing a greater support service for young professors and PhD students that will help in the development of their academic careers.