bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability of the viscous flow of a polymeric fluid past a flexible surface
Authors: Chokshi Paresh , Kumaran V.
Published: March 2007

The instability in plane Couette flow of a viscoelastic fluid past a deformable surface is examined using the temporal linear stability theory in the zero Reynolds number limit. The polymeric fluid is described using the Oldroyd-B model and the flexible wall is modeled as a linear viscoelastic solid surface. The analysis shows that the wall flexibility tends to reduce the decay rate of the stable discrete modes for the polymeric flow past a rigid wall, and one of the discrete modes becomes unstable when the wall deformability parameter Γ=Vη∕(GR) exceeds a certain critical value Γc. Here, V is the top-plate velocity, η is the zero shear viscosity of the polymeric fluid, G is the shear modulus of the wall, and R is the width of the fluid layer. The analysis reveals the presence of two classes of modes, the first of which becomes unstable for perturbations with wavelength comparable to the channel width (finite wavelength modes), and the second becomes unstable for perturbations with wavelength small compared to the channel width (short wave modes). The latter class of modes are found to be absent for the highly concentrated polymer solutions with β≲0.23, where β is the ratio of solvent-to-solution viscosity. We have mapped out the regions in the parameter space (W¯-H) where the finite wavelength and short wave modes are unstable, where W¯=(λG∕η), and λ is the relaxation time of the viscoelastic fluid. Fluid elasticity is found to have a stabilizing influence on the unstable mode, such that when the shortwave instability is absent for β≲0.23, the flow becomes stable for any Weissenberg number W¯>W¯max. Here, W¯max increases proportional to H for H≫1. However, when the shortwave instability is present, the instability persists for W¯≫1. The behavior of both classes of modes with respect to the parameters, like W¯, H, β, and the ratio of solid-to-fluid viscosity ηr, is examined.
Dynamical properties of a dissipative hybrid Fermi-Ulam-bouncer model
Authors: Ladeira Denis G. , Leonel Edson D.
Published: March 2007

Some consequences of dissipation are studied for a classical particle suffering inelastic collisions in the hybrid Fermi-Ulam bouncer model. The dynamics of the model is described by a two-dimensional nonlinear area-contracting map. In the limit of weak and moderate dissipation we report the occurrence of crisis and in the limit of high dissipation the model presents doubling bifurcation cascades. Moreover, we show a phenomena of annihilation by pairs of fixed points as the dissipation varies.
Independent electron model for open quantum systems: Landauer-Büttiker formula and strict positivity of the entropy production
Authors: Nenciu Gheorghe
Published: March 2007

A general argument leading from the formula for currents through an open noninteracting mesoscopic system given by the theory of nonequilibrium steady states to the Landauer-Büttiker formula is pointed out. Time reversal symmetry is not assumed. As a consequence it is shown that, as far as the system has a nontrivial scattering theory and the reservoirs have different temperatures and/or chemical potentials, the entropy production is strictly positive.
Art of war hidden in Kolmogorov’s equations
Authors: Lauren Michael K. , McIntosh Gregory C. , Perry Nigel , Moffat James
Published: March 2007

Here we discuss how Kolmogorov’s work on turbulence can be used as the inspiration for a new description of battlefield dynamics. The method presented may also represent a new way of describing self-organizing dynamical systems, in place of conventional differential equation approaches. The key finding is that the rate of attrition in a battle appears to be a function of the fractal dimension of the opposing forces. It is suggested that, this being the case, the fractal dimension could be used as a surrogate to represent the organizational efficiency of one force relative to another, commonly called Command and Control.
Photoexcited Fano interaction in laser-etched silicon nanostructures
Authors: Kumar Rajesh , Mavi H. S. , Shukla A. K. , Vankar V. D.
Published: March 2007

Photoexcitation dependent Raman studies on the optical phonon mode in silicon nanostructures (Si NS) prepared by laser-induced etching are done here. The increase in the asymmetry of the Raman spectra on the increasing laser power density is attributed to Fano interference between discrete optical phonons and continuum of electronic excitations in the few nanometer size nanoparticles made by laser-induced etching. No such changes are observed for the same laser power density in the crystalline silicon sample or ion-implanted silicon sample followed by laser annealing. A broad photoluminescence spectrum from Si NS contains multiple peak behavior, which reveals the presence of continuum of electronic states in the Si NS.
Electrical and Raman characterization of silicon and germanium-filled microstructured optical fibers
Authors: Finlayson C. E. , Amezcua-Correa A. , Sazio P. J. A. , Baril N. F. , Badding J. V.
Published: March 2007

Extreme aspect ratio tubes and wires of polycrystalline silicon and germanium have been deposited within silica microstructured optical fibers using high-pressure precursors, demonstrating the potential of a platform technology for the development of in-fiber optoelectronics. Microstructural studies of the deposited material using Raman spectroscopy show effects due to strain between core and cladding and the presence of amorphous and polycrystalline phases for silicon. Germanium, in contrast, is more crystalline and less strained. This in-fiber device geometry is utilized for two- and three-terminal electrical characterization of the key parameters of resistivity and carrier type, mobility and concentration.
A direct relation between the filtered subgrid stress and the second order structure function
Authors: Germano M.
Published: March 2007

In this Brief Communication we rewrite the filtered subgrid stress in terms of velocity increments and we directly relate its mean value to the second order structure function.
Conduction band offset for Ga0.62In0.38NxAs0.991−xSb0.009∕GaNyAs1−y∕GaAs systems with the ground state transition at 1.5–1.65μm
Authors: Kudrawiec R. , Bank S. R. , Yuen H. B. , Bae H. , Wistey M. A. , Goddard L. L. , Harris James S. , Gladysiewicz M. , Motyka M. , Misiewicz J.
Published: March 2007

Conduction band offset for Ga0.62In0.38NxAs0.991−xSb0.009∕GaNyAs1−y∕GaAs systems with different N contents (x=2.2%–3.0% and y=3.1%–4.3% of N) has been investigated by contactless electroreflectance spectroscopy supported by theoretical calculations performed within the effective mass approximation. It has been found that Ga0.62In0.38NxAs0.991−xSb0.009∕GaNyAs1−y quantum wells (QWs) are promising for laser applications from the point of view of carrier confinement since the conduction band offset (QC) for these QWs is between 70% and 75%. In addition, it has been shown that GaNAs∕GaAs interface is type I with QC between 80% and 90%.
Measurement of carrier concentration captured by InAs∕GaAs quantum dots using terahertz time-domain spectroscopy
Authors: Oh Seung Jae , Kang Chul , Maeng Inhee , Son Joo-Hiuk , Cho Nam Ki , Song Jin Dong , Choi Won Jun , Cho Woon-Jo , Lee Jung Il
Published: March 2007

The authors investigated the carrier dynamics of n-type modulation-doped InAs∕GaAs quantum dots (QDs) using terahertz time-domain spectroscopy to estimate the total number of electrons captured by the QDs. The terahertz power absorption of the sample with QDs was less than that of the sample without QDs. This is attributed to the fact that the carriers are confined in the QDs. The experiment results were fitted into the Drude model and the number of electrons captured by QDs was determined through the difference in the numbers of free electrons of the samples with and without QDs.
Simple voltage tunable liquid crystal laser
Authors: Blinov L. M. , Cipparrone G. , Mazzulla A. , Pagliusi P. , Lazarev V. V. , Palto S. P.
Published: March 2007

Lasing has been observed in a dye-doped liquid crystal placed between one substrate with a large transparent electrode and the other with a system of parallel nontransparent electrode stripes of 15μm period. The stripes operate as a shadow mask providing the spatial modulation of the pump beam and material gain and, with the voltage applied, it additionally creates a Bragg resonator structure due to the spatial modulation of refraction. With that simple cell, a voltage induced tuning of the spectral positions of laser lines over 25nm has been demonstrated.
Laser direct writing carbon nanotube arrays on transparent substrates
Authors: Chen Zhuo , Wei Yang , Luo Chunxiang , Jiang Kaili , Zhang Lina , Li Qunqing , Fan Shoushan , Gao Jiancun
Published: March 2007

The authors report the synthesis of multiwalled carbon nanotubes on transparent substrates by utilizing a diode laser to locally heat the catalysts to high temperature. Well-aligned bamboo-shaped multiwalled carbon nanotubes can be synthesized on glass substrate covered with a carbon black layer. If the carbon black was substituted by the commercial graphite inner coating, randomly oriented but high quality multiwalled carbon nanotubes were obtained with excellent field emission performance. This approach facilitates the fabrication of multiwalled carbon nanotube field emitters for field emission flat panel displays without limitations on the geometry size and temperature requirement of the substrate.
Improving spatial resolution of two-photon microfabrication by using photoinitiator with high initiating efficiency
Authors: Xing Jin-Feng , Dong Xian-Zi , Chen Wei-Qiang , Duan Xuan-Ming , Takeyasu Nobuyuki , Tanaka Takuo , Kawata Satoshi
Published: March 2007

The lateral spatial resolution (LSR) in two-photon induced polymerization was improved to 80nm by using an anthracene derivative (9,10-bis-pentyloxy-2,7-bis[2-(4-dimethylamino-phenyl)-vinyl]anthracene (BPDPA)) as a highly sensitive and efficient photoinitiator. Photocurable resin containing 0.18mol% BPDPA exhibited a low polymerization threshold of 0.64mW at 800nm. Theoretical calculations showed that the LSR can be increased by reducing the laser power, indicating that the LSR could be improved using more sensitive initiators in the future.
Efficient particle labeling in atomistic simulations
Authors: Meloni Simone , Rosati Mario , Colombo Luciano
Published: March 2007

The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme.
Increased density, biomass and egg production in an unfished population of Western Rock Lobster (Panulirus cygnus) at Rottnest Island, Western Australia
Authors: Babcock R. C. , Phillips J. C. , Lourey M. , Clapin G.
Published: March 2007

Surveys of spiny lobster (Panulirus cygnus) populations in shallow waters surrounding Rottnest Island in Western Australia revealed much higher levels of density, biomass and egg production in no-take than in fished areas. Density of lobsters was ~34 times higher in the sanctuary, and density of lobsters above minimum legal size around 50 times higher than in other areas around the island where recreational fishing is allowed. Mean carapace length (CL), total biomass and egg production of lobsters in the sanctuary zone were significantly higher than in adjacent fished areas. Large individuals (≥100 mm CL), especially large males, were found almost exclusively within the sanctuary. The abundance of mature animals in these shallow waters indicates that not all P. cygnus migrate to deep water and that shallow water habitats may currently be well below carrying capacity in terms of biomass and egg production. If implemented in a systematic way, unfished areas such as the Kingston Reefs could also provide a useful fisheries-independent tool for assessing trophic interactions and the structure and density of unfished populations, and for estimating parameters such as growth of larger individuals that may be rare or absent in more widely fished populations.
Assessing the need for sequence-based normalization in tiling microarray experiments
Authors: Royce Thomas E. , Rozowsky Joel S. , Gerstein Mark B.
Published: March 2007

Motivation: Increases in microarray feature density allow the construction of so-called tiling microarrays. These arrays, or sets of arrays, contain probes targeting regions of sequenced genomes at regular genomic intervals. The unbiased nature of this approach allows for the identification of novel transcribed sequences, the localization of transcription factor binding sites (ChIP-chip), and high resolution comparative genomic hybridization, among other uses. These applications are quickly growing in popularity as tiling microarrays become more affordable. To reach maximum utility, the tiling microarray platform needs be developed to the point that 1 nt resolutions are achieved and that we have confidence in individual measurements taken at this fine of resolution. Any biases in tiling array signals must be systematically removed to achieve this goal.

Results: Towards this end, we investigated the importance of probe sequence composition on the efficacy of tiling microarrays for identifying novel transcription and transcription factor binding sites. We found that intensities are highly sequence dependent and can greatly influence results. We developed three metrics for assessing this sequence dependence and use them in evaluating existing sequence-based normalizations from the tiling microarray literature. In addition, we applied three new techniques for addressing this problem; one method, adapted from similar work on GeneChip brand microarrays, is based on modeling array signal as a linear function of probe sequence, the second method extends this approach by iterative weighting and re-fitting of the model, and the third technique extrapolates the popular quantile normalization algorithm for between-array normalization to probe sequence space. These three methods perform favorably to existing strategies, based on the metrics defined here.

Availability:  http://tiling.gersteinlab.org/sequence_effects/

Contact:  mark.gerstein@yale.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Cytoprotective Activity of Glycyrrhizae radix Extract against Arsenite‐Induced Cytotoxicity
Authors: Kim Sang Chan , Park Sook Jahr , Lee Jong Rok , Seo Jung Cheol , Yang Chae Ha , Byun Sung Hui
Published: March 2007

Licorice, Glycyrrhizae radix, is one of the herbal medicines in East Asia that has been commonly used for treating various diseases, including stomach disorders. This study investigated the effect of licorice on arsenite (As)‐induced cytotoxicity in H4IIE cells, a rat hepatocyte‐derived cell line. Cell viability was significantly diminished in As‐treated H4IIE cells in a time and concentration‐dependent manner. Furthermore, results from flow cytometric assay and DNA laddering in H4IIE cells showed that As treatment induced apoptotic cell death by activating caspase‐3. Licorice (0.1 and 1.0 mg ml−1) treatment significantly inhibited cell death and the activity of caspase‐3 in response to As exposure. These results demonstrate that licorice induced a cytoprotective effect against As‐induced cell death by inhibition of caspase‐3.
Ballooning dispersal in arthropod taxa: conditions at take-off
Authors: Reynolds Andy M , Bohan David A , Bell James R
Published: March 2007

We have solved a long-standing and seemingly paradoxical set of questions that relate to the conditions which govern spider ballooning. We show that observations of spider ballooning excursions are best explained by meteorological conditions which maximize dispersal. Dispersal is predicted to be most effective in terms of distance when the stability of the atmosphere is non-ideally convective and is less effective during purely convective or neutrally stable conditions. Ballooners are most likely to travel a few hundred metres, but dispersal distances of several hundred kilometres are possible.
Robert Hooke's ‘universal joint’ and its application to sundials and the sundial-clock
Authors: Mills Allan
Published: March 2007

Robert Hooke is commonly thought of as the inventor of ‘Hooke's joint’ or the ‘universal joint’. However, it is shown that this flexible coupling (based on a four-armed cross pivoted between semicircular yokes attached to two shafts) was in fact known long before Hooke's time but was always assumed to give an output exactly matching that of the input shaft. Hooke carefully measured the relative displacements of the two axes, and found that if one were inclined to the other, uniform rotation of the input produced a varying rate of rotation of the output. He also recognized that this variable rate exactly corresponded to the movement of the shadow of a gnomon across the face of a sundial, as generated by the projection of the uniform motion of the Sun around an inclined polar axis. He therefore proposed that a ‘mechanical sundial’ might be made by coupling a 24-hour clock movement (with its hour shaft at the appropriate inclination) to a pointer via a universal joint. This proposal has been investigated both practically and mathematically, and shown to be valid. Hooke's studies of the universal joint caused it to be identified with his name, and it has ultimately proved far more important as a rotary coupling than as a sundial analogue. More complex versions subsequently designed by Hooke included provision for two basic couplings to be linked by an intermediate shaft. With appropriate setting of phase and shaft angles this ‘double Hooke's joint’ could annul the variable output velocity characteristic of the single universal. It has proved invaluable for modern automotive transmissions.
Composition of an avian guild in spatially structured habitats supports a competition–colonization trade-off
Authors: Rodríguez Alejandro , Jansson Gunnar , Andrén Henrik
Published: March 2007

Assuming better colonization abilities of inferior competitors, the competition–colonization trade-off (CCTO) is one of the hypotheses that explains spatial variation of species composition in fragmented habitats. Whereas this mechanism may structure some plant and insect communities, ecologists have failed to document its operation in other natural systems, and its generality has been questioned. We combined fieldwork and published data to study the composition of a guild of passerines (
Parus cristatus
,
Parus montanus
,
Parus ater
and
Regulus regulus
) inhabiting 10 landscapes that differed in the amount of forest habitat. The species were ordered in a stable, well-defined competitive hierarchy, and the dispersal ability of each species was inversely correlated with its position in this hierarchy. In functionally continuous landscapes, superior competitors occupied most fragments and all guild members commonly occurred. The relative incidences of superior and inferior competitors were reversed, and differences amplified, in landscapes where patches were physically (distance) or functionally (matrix hardness) isolated. We found little support for two competing hypotheses, namely reduced habitat quality in isolated patches and lower abundance of a keystone predator (
Glaucidium passerinum
) in fragmented landscapes. We concluded that the CCTO offered the most probable explanation for variation in the composition of the
Parus
guild across landscapes.
Specialization in policing behaviour among workers in the ant
Pachycondyla inversa
Authors: van Zweden Jelle S , Fürst Matthias A , Heinze Jürgen , D'Ettorre Patrizia
Published: March 2007

Most animal societies are non-clonal and thus subject to conflicts. In social insects, conflict over male production can be resolved by worker policing, i.e. eating of worker-laid eggs (WLE) or aggression towards reproductive workers. All workers in a colony have an interest in policing behaviour being expressed, but there can be asymmetries among workers in performing the actual behaviour. Here, we show that workers of the ant
Pachycondyla inversa
specialize in policing behaviour. In two types of behavioural assays, workers developed their ovaries and laid eggs. In the first experiment, reproductive workers were introduced into queenright colonies. In the second experiment, WLE were introduced. By observing which individuals policed, we found that aggressive policing was highly skewed among workers that had opportunity to police, and that a similar tendency occurred in egg policing. None of the policing workers had active ovaries, so that policing did not incur a direct selfish benefit to the policer. This suggests that policing is subject to polyethism, just like other tasks in the colony. We discuss several hypotheses on the possible causes of this skew in policing tasks. This is the first non-primate example of specialization in policing tasks without direct selfish interests.
Sulfitobacter litoralis sp. nov., a marine bacterium isolated from the East Sea, Korea
Authors: Park Ja Ryeong , Bae Jin-Woo , Nam Young-Do , Chang Ho-Won , Kwon Hyuk-Yong , Quan Zhe-Xue , Park Yong-Ha
Published: March 2007

A Gram-negative, aerobic, halophilic bacterium, designated strain Iso 3T, was isolated from the East Sea in Korea. Strain Iso 3T was motile by means of polar flagella, occasionally formed rosette-like aggregates and contained 18 : 1ω7c as the dominant cellular fatty acid. Strain Iso 3T grew at NaCl concentrations of 1–10 % and temperatures of 4–30 °C. The optimal growth temperature was 20 °C. Analysis of the 16S rRNA gene sequence revealed that this strain is affiliated with a subcluster of the Alphaproteobacteria. However, strain Iso 3T generated metabolic energy by sulfide oxidation. The 16S rRNA gene sequence similarity between strain Iso 3T and the type strain of the most closely related species, Sulfitobacter pontiacus, was 97.7 %. DNA–DNA relatedness between strain Iso 3T and Sulfitobacter pontiacus DSM 10014T was 24.1 %. On the basis of phenotypic properties and phylogenetic distinctiveness, strain Iso 3T is classified within a novel Sulfitobacter species, for which the name Sulfitobacter litoralis sp. nov. is proposed, with the type strain Iso 3T (=KCTC 12521T=DSM 17584T).
Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil
Authors: Ahmed Iftikhar , Yokota Akira , Fujiwara Toru
Published: March 2007

A motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16XT, produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16–37 °C (optimum 25–28 °C) and the pH range for growth was 6.0–10.0 (optimum pH 7.5–8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C15 : 0and anteiso-C15 : 0at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system andmeso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains ofGracilibacillus orientalis(96.7 % similarity),G. halotolerans(95.5 %) andG. dipsosauri(95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16XT(=DSM 17256T=IAM 15263T=ATCC BAA-1190T) is proposed to be a member of the genusGracilibacillusas the type strain of the novel speciesGracilibacillus boraciitoleranssp. nov.
Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell
Authors: Holmes Dawn E. , Nevin Kelly P. , Woodard Trevor L. , Peacock Aaron D. , Lovley Derek R.
Published: March 2007

A Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2T) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2T does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4–42 °C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2T represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2T. Results from physiological, biochemical and phylogenetic analyses showed that strain F2T should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2T (=ATCC BAA-1284T=JCM 13498T).
Haloferax larsenii sp. nov., an extremely halophilic archaeon from a solar saltern
Authors: Xu Xue-Wei , Wu Yue-Hong , Wang Chun-Sheng , Oren Aharon , Zhou Pei-Jin , Wu Min
Published: March 2007

Three strains of Gram-negative, aerobic, neutrophilic, extremely halophilic archaea, designated ZJ206T, ZJ203 and ZJ204, were isolated from a solar saltern in Zhe-Jiang Province, China. Phenotypically and on the basis of 16S rRNA gene sequences, the strains were very similar. Comparative 16S rRNA gene analysis revealed 96.4–97.4 % sequence similarity to members of the genus Haloferax. The major polar lipids were C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, diglycosyl glycerol diether and sulfated diglycosyl diether. The DNA G+C content of strain ZJ206T was 62.2 mol%. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Therefore the isolates should be classified as members of a novel species, for which the name Haloferax larsenii sp. nov. is proposed. The type strain is ZJ206T (=CGMCC 1.5347T=JCM 13917T).
Nocardioides marinus sp. nov.
Authors: Choi Dong Han , Kim Hye Min , Noh Jae-Hoon , Cho Byung Cheol
Published: March 2007

A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).
Natronorubrum sulfidifaciens sp. nov., an extremely haloalkaliphilic archaeon isolated from Aiding salt lake in Xin-Jiang, China
Authors: Cui Heng-Lin , Tohty Dilbr , Liu Hong-Can , Liu Shuang-Jiang , Oren Aharon , Zhou Pei-Jin
Published: March 2007

An extremely haloalkaliphilic archaeon, strain AD2T, was isolated from Aiding salt lake in Xin-Jiang, China. Strain AD2T required at least 12 % NaCl for growth. MgCl2 was not required. The isolate was able to grow over a pH range of 8.0–10.0 and temperature range of 20–55 °C, with optimal growth at pH 8.7–9.2 and 44–47 °C. The major polar lipids of strain AD2T were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; glycolipids were not detected. Analysis of its 16S rRNA gene sequence indicated that strain AD2T was phylogenetically related to members of the genus Natronorubrum, with sequence similarities to the type strains of Natronorubrum bangense, Natronorubrum tibetense and Natronorubrum aibiense of 97.1, 95.9 and 96.1 %, respectively. The G+C content of its DNA was 60.9 mol% (T
m). Levels of DNA–DNA relatedness between strain AD2T and the type strains of Nrr. bangense, Nrr. tibetense and Nrr. aibiense were 49, 38 and 41 %, respectively. It was concluded that strain AD2T represents a novel species of the genus Natronorubrum, for which the name Natronorubrum sulfidifaciens sp. nov. is proposed. The type strain is AD2T (=CGMCC 1.6307T=JCM 14089T).
Description of Pseudochrobactrum kiredjianiae sp. nov.
Authors: Kämpfer Peter , Scholz Holger , Huber Birgit , Thummes Kathrin , Busse Hans-Jürgen , Maas Elizabeth W. , Falsen Enevold
Published: March 2007

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain CCUG 49584T), isolated from a seafood processing plant sample in New Zealand, was subjected to a polyphasic taxonomic study. On the basis of 16S rRNA and recA gene sequence similarities, the isolate was allocated to the genus Pseudochrobactrum. This was confirmed by fatty acid data (major fatty acids: C18 : 1
ω7c and C19 : 0 cyclo ω8c), a polar lipid profile exhibiting major characteristics of Pseudochrobactrum (phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine), quinone system Q-10 and a polyamine pattern with the predominant compounds spermidine and putrescine. DNA–DNA hybridization with the type strains of the two established species of Pseudochrobactrum and physiological and biochemical data clearly differentiated the isolate from established Pseudochrobactrum species. As a consequence, this organism represents a novel species, for which the name Pseudochrobactrum kiredjianiae sp. nov. is proposed, with the type strain CCUG 49584T (=CIP 109227T).
Vagococcus elongatus sp. nov., isolated from a swine-manure storage pit
Authors: Lawson Paul A. , Falsen Enevold , Cotta Michael A. , Whitehead Terence R.
Published: March 2007

A polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-manure storage pit. The bacterium, designated strain PPC9T, was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9T was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9T is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9T (=CCUG 51432T=NRRL B-41357T).
Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue
Authors: Endo Akihito , Okada Sanae
Published: March 2007

Two strains of lactic acid bacteria, strains NRIC 0689T and NRIC 0690, were isolated from a compost of distilled shochu residue in Japan. The isolates showed quite low sequence similarity to known species of lactic acid bacteria on the basis of 16S rRNA gene sequence; the highest sequence similarities to NRIC 0689T were shown by the type strains of Lactobacillus satsumensis, L. plantarum, L. hilgardii, L. buchneri and L. parabuchneri (92.9, 92.9, 92.8, 92.6 and 92.5 %, respectively). The isolates formed a distinct subcluster in the Lactobacillus casei–Pediococcus phylogenetic cluster. Levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon. Therefore, the isolates represent a novel species, for which the name Lactobacillus composti sp. nov. is proposed. The type strain is NRIC 0689T (=JCM 14202T=DSM 18527T).
Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier
Authors: Zhang De-Chao , Wang He-Xiang , Cui Heng-Lin , Yang Yong , Liu Hong-Can , Dong Xiu-Zhu , Zhou Pei-Jin
Published: March 2007

A novel psychrotolerant, Gram-positive, yellow-pigmented, aerobic bacterium, strain 0549T, was isolated from the China No. 1 glacier. The cells of the isolate were catalase-positive, motile, irregular rods. The diamino acid content of the cell-wall peptidoglycan was determined to be 2,4-diaminobutyric acid. Strain 0549T was able to grow at 4–27 °C, with optimum growth occurring at 20–22 °C. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 67 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 0549T belonged to the genus Cryobacterium and exhibited 96.5 % similarity to Cryobacterium psychrophilum JCM 1463T. On the basis of the phenotypic, chemotaxonomic and phylogenetic properties and the DNA–DNA relatedness data, strain 0549T represents a novel species of the genus Cryobacterium, for which the name Cryobacterium psychrotolerans is proposed. The type strain is 0549T (=CGMCC 1.5382T=JCM 13925T).
Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan
Authors: Suzuki Daisuke , Ueki Atsuko , Amaishi Aya , Ueki Katsuji
Published: March 2007

Two strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1T and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1T and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H2 as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1T and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H2). Major cellular fatty acids of both strains were C15 : 0, C16 : 0, C17 : 1
ω6 and C18 : 1
ω7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria. The closest recognized relative of strains Pro1T and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1T and Pro16 represent a novel species of the genus Desulfobulbus, for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1T(=JCM 14043T=DSM 18378T) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
Authors: Ponjavic Jasmina , Ponting Chris P. , Lunter Gerton
Published: March 2007

Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby leaving an impression that, instead, they represent “transcriptional noise.” Here, we describe an analysis of 3122 long and full-length, noncoding RNAs (“macroRNAs”) from the mouse, and compare their sequences and their promoters with orthologous sequence from human and from rat. We considered three independent signatures of purifying selection related to substitutions, sequence insertions and deletions, and splicing. We find that the evolution of the set of noncoding RNAs is not consistent with neutralist explanations. Rather, our results indicate that purifying selection has acted on the macroRNAs’ promoters, primary sequence, and consensus splice site motifs. Promoters have experienced the greatest elimination of nucleotide substitutions, insertions, and deletions. The proportion of conserved sequence (4.1%–5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs’ functions.
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
Authors: Kikuta Hiroshi , Laplante Mary , Navratilova Pavla , Komisarczuk Anna Z. , Engström Pär G. , Fredman David , Akalin Altuna , Caccamo Mario , Sealy Ian , Howe Kerstin , Ghislain Julien , Pezeron Guillaume , Mourrain Philippe , Ellingsen Staale , Oates Andrew C. , Thisse Christine , Thisse Bernard , Foucher Isabelle , Adolf Birgit , Geling Andrea , Lenhard Boris , Becker Thomas S.
Published: March 2007

We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated “bystander” genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs.
Sprouty2 regulates growth and differentiation of human neuroblastoma cells through RET tyrosine kinase
Authors: Ishida Maki , Ichihara Masatoshi , Mii Shinji , Jijiwa Mayumi , Asai Naoya , Enomoto Atsushi , Kato Takuya , Majima Ai , Ping Jiang , Murakumo Yoshiki , Takahashi Masahide
Published: March 2007

The Sprouty (SPRY) family of proteins includes important regulators of downstream signaling initiated by receptor tyrosine kinases. In the present study, we investigated the role of SPRY proteins in intracellular signaling via the RET receptor tyrosine kinase activated by glial cell line‐derived neurotrophic factor (GDNF). Expression of SPRY1, SPRY2, SPRY3 and SPRY4 in HEK293T cells transfected with RET and GDNF receptor family α1 (GFRα1) genes significantly reduced sustained ERK activation as well as ELK‐1 activation. Because expression of SPRY2 was efficiently induced by GDNF in TGW human neuroblastoma cells expressing RET and GFRα1, we further investigated the role of SPRY2 in the growth and differentiation of TGW cells. Expression of wild‐type SPRY2 (WT‐SPRY2) decreased the growth of TGW cells. In contrast, expression of a dominant negative form of SPRY2 (MT‐SPRY2, with a mutated tyrosine residue) enhanced cell proliferation. In addition, expression of WT‐SPRY2 reduced GDNF‐dependent neurite outgrowth of TGW cells, whereas expression of MT‐SPRY2 enhanced it. Taken together, our results suggest that SPRY2 regulates GDNF‐dependent proliferation and differentiation of TGW neuroblastoma cells mediated by RET tyrosine kinase. (Cancer Sci 2007; 98: 815–821)
Pseudomonas corrugata: plant pathogen and/or biological resource?
Authors: CATARA VITTORIA
Published: March 2007

Pseudomonas corrugata is the causal agent of tomato pith necrosis yet it is also used in the biological control of plant pathogenic bacteria and fungi. Potentially it could be used in other fields, such as the production of commercial biomolecules with a wide range of application and including bioremediation. This review reports the multiple characteristics of the bacterium, highlights its known molecular features and speculates on the possible underlying mechanisms of action.

Taxonomy:  Bacteria; Proteobacteria; γ subdivision; order Pseudomonadales; family Pseudomonadaceae; genus Pseudomonas.

Microbiological properties:  Gram‐negative, oxidase‐positive, non‐spore forming rods; non‐fluorescent on King's B medium; produces wrinkled and rarely smooth colonies on yeast peptone glucose agar or nutrient dextrose agar; yellow to brown diffusible pigments are frequently produced.

Disease symptoms:  The typical symptom on tomato is necrosis and/or hollowing of the pith of the stem; the syndrome determines loss of turgidity of the plant, hydropic/necrotic areas and long conspicuous adventitious roots on the stem.

Biological control agent: In vitro assessed against plant pathogenic fungi and bacteria, as well as the phytotoxin indicator microorganims Rhodotorula pilimanae and Bacillus megaterium; in vivo used against pre‐ and post‐harvest plant pathogens.
Co‐existent Langerhans cell histiocytosis and Rosai–Dorfman disease: a diagnostic rarity
Authors: Sachdev R. , Shyama J.
Published: March 2007

Co‐existent Langerhans cell histiocytosis and Rosai–Dorfman disease: a diagnostic rarity
Haemorrhagic cytology samples – how to get the best diagnostic results
Authors: Srebotnik Kirbiš I. , Strojan Fležar M. , Lavrenčak J. , Pohar Marinšek Ž.
Published: March 2007

Objective:  To describe and evaluate the value of a simple filtration technique for use in processing haemorrhagic samples for cytomorphological evaluation and immunocytochemistry.

Methods:  One hundred and sixty haemorrhagic cytological samples (133 FNAs, 27 effusions) received in our laboratory from August 2002 to September 2005 were included in this study. After preparing two smears for diagnostic evaluation, the residual sample was suspended in 2 ml of a cell medium prepared in our laboratory. These primary haemorrhagic suspensions were filtered through disposable nylon filter devices and the cells deposited on the upper membrane surface were transferred into 2 ml of fresh cell medium. From all three fractions – primary cell suspension, filter deposit and filtrate – cytospins were prepared and stained by Giemsa or Papanicolaou methods. Cytospins were examined under the microscope for the presence of diagnostic cells, red blood cells (RBCs) and debris. Additional cytospins for immunocytochemistry were prepared at the cytopathologist's request.

Results:  RBCs and debris were successfully removed in 142 out of 160 haemorrhagic samples (88%) by using this new filtration technique. In all these cases the tumour cells were well presented and allowed substantially improved cytomorphological evaluation. Immunocytochemical staining was performed on 112 filtered samples with three different markers per case on average. Filtration did not improve the quality of cytospins in 18/160 haemorrhagic samples, mostly attributable to insufficient numbers of diagnostic cells in the original samples.

Conclusion:  The presented filtration technique is very simple and quick. It substantially improves the quality of haemorrhagic samples for cytomorphological evaluation; moreover, the samples are well suited for multiple immunocytochemical stainings.
Cumulative sum procedure in evaluation of EUS‐guided FNA cytology: the learning curve and diagnostic performance beyond sensitivity and specificity
Authors: Eltoum I. A. , Chhieng D. C. , Jhala D. , Jhala N. C. , Crowe D. R. , Varadarajulu S. , Eloubeidi M. A.
Published: March 2007

Background:  Using cumulative sum (CUSUM) chart, we address two questions: (i) Over time, how will an EUS‐FNA (endoscopic ultrasound guided fine needle aspiration) service maintain an acceptable non‐diagnostic rate defined as technical failures, unsatisfactory specimens and atypical and suspicious diagnoses? (ii) Over time, how will EUS‐FNA maintain acceptable diagnostic errors (false‐positives plus false‐negative diagnosis)?

Methods:  The study included all consecutive patients who underwent EUS‐FNA at our institution from July 2000 to October 2003 and were followed up until December 2004. Using a simple spread sheet, we designed CUSUM charts and used them to track trends and assess performance at a preset acceptable rate of 10% and a preset unacceptable rate of 15% for non‐diagnostic rate and diagnostic errors. We assessed all cases collectively and then in groups defined by site, size and cytopathologist.

Results:  Of 876 patients undergoing EUS‐FNA, 83 (9.5%) had non‐diagnostic results: 43 (51%) of these diagnoses were ‘atypical’, 27(33%) were ‘suspicious for malignancy’, eight (10%) were ‘insufficient material for diagnosis’ and five (6%) were ‘technical failure’. In 585 cases with adequate follow up, there were 26 (6.3%) diagnostic errors: three (0.5%) were false positive and 23 (3.1) were false negative. The overall CUSUM charts for both non‐diagnostic rate and for diagnostic error rate start with a small period of learning then cross to a significantly acceptable level at case numbers 121 and 97 respectively. Our diagnostic performance was better in lymph nodes than in the pancreas and other organs and was not significantly different for lesions ≤25 mm compared with lesion >25 mm in diameter. Performance was better for pathologists with prior experience than for pathologists without experience.

Conclusion:  In the current climate of proficiency testing, error tracking and competence evaluation, there is a great potential for the use of CUSUM charts to assess procedure failure and error tracking in quality control programs, particularly when a new procedure such as EUS‐FNA is introduced in the laboratory. Additionally, the method can be used to assess trainee competency and to track the proficiency of practicing cytologists.