bluuebunny/crossref_metadata_2025 huggingface dataset:
Viscoelastic effects on higher order statistics and on coherent structures in turbulent channel flow
Authors: Housiadas Kostas D. , Beris Antony N. , Handler Robert A.
Published: February 2005

In this work we study, using the results of direct numerical simulations [Housiadas and Beris, “Polymer-induced drag reduction: Viscoelastic and inertia effects of the variations in viscoelasticity and inertia,” Phys. Fluids 15, 2369 (2003)], the effects of changes in the flow viscoelasticity and the friction Reynolds number on several higher order statistics of turbulence, such as the Reynolds stress, the enstrophy, the averaged equations for the conformation tensor, as well as on the coherent structures through a Karhunen–Loeve (K-L) analysis and selected flow and conformation visualizations. In particular, it is shown that, as the zero friction Weissenberg number Weτ0 increases (for a constant zero friction Reynolds number Reτ0) dramatic reductions take place in many terms in the averaged equations for the Reynolds stresses and in all terms of the averaged enstrophy equations. From a Karhunen–Loeve analysis of the eigenmodes of the flow we saw that the presence of viscoelasticity increases significantly the coherence and energy content of the first few modes. The K-L dimension of the flow at Weτ0=125 is fully one order of magnitude lower than its Newtonian counterpart. As far as the effect of viscoelasticity is concerned, it is manifested primarily by changes in the boundary layer, which are mostly accomplished by Weτ0=50–62.5. In comparison, increasing the Reτ0, from 125 to 590, induces significant changes in various terms in the budgets, despite the fact that the drag reduction remains practically the same over that range. However, the near the wall region seems to change significantly only up to Reτ0=395, with few changes observed upon a further increase to Reτ0=590.
Size-dependent switching of multilayer magnetic elements
Authors: Ross C. A. , Castaño F. J. , Rodriguez E. , Haratani S. , Vögeli B. , Smith Henry I.
Published: February 2005

Pseudo-spin-valve NiFe∕Cu∕NiFe, Co∕Cu∕Co, NiFe∕Cu∕Co films and magnetic tunnel junction films have been patterned into arrays of rectangular elements with widths of 40–140nm and aspect ratios of 1.5–18. The switching field of the hard and soft layers and the interaction field between the layers have been measured as a function of aspect ratio. In the pseudo-spin-valve structures the behavior is dominated by magnetostatic interactions between the layers, leading to antiparallel alignment of the hard and soft layers at remanence for small aspect ratios. Patterned tunnel junction films show weaker magnetostatic effects, and the exchange bias from the antiferromagnetic layer is preserved on patterning.
Sharp scalar and tensor bounds on the hydrodynamic friction and mobility of arbitrarily shaped bodies in Stokes flow
Authors: Blawzdziewicz J. , Wajnryb E. , Given J. A. , Hubbard J. B.
Published: February 2005

We prove rigorous inequalities for the hydrodynamic translational friction and mobility matrices ζ and μO of an arbitrarily shaped rigid particle in terms of the electrostatic capacitance C of a conducting particle of identical shape. Specifically, we derive the scalar and matrix inequalities 13trζ−1⩽13trμO⩽C−1 and 23ζ−1⩽C−1I, where all quantities are normalized by the corresponding values for a sphere, and the mobility matrix is evaluated in the center-of-mobility reference frame. These bounds are obtained using a variational approach with the energy dissipation functional expressed in terms of the induced force distribution on the surface of the particle. To relate the hydrodynamic problem to the solution of the corresponding electrostatic problem, the trial force field is expressed in terms of the charge distribution on the equipotential particle surface. This procedure yields the first rigorous bounds on hydrodynamic friction that apply to bodies with translation-rotation coupling. We demonstrate that the error of the Hubbard–Douglas approximation 13trζ−1≈C−1, corresponding to our scalar bound, is quadratic in the deviation of the trial induced-force field from the exact form—which explains why this relation is highly accurate for many particle shapes. Our numerical results confirm that the Hubbard–Douglas approximation is accurate for a variety of objects, including helices with translational–rotational coupling. In addition, we establish a rigorous, sharp bound on the effective (scalar) Brownian diffusion coefficient of an arbitrarily shaped particle.
Mesofrequency switching dynamics in epitaxial CoFe and Fe thin films on GaAs(001)
Authors: Moore T. A. , Walker M. J. , Middleton A. S. , Bland J. A. C.
Published: February 2005

Thin epitaxial Co27Fe73 and Fe films have been grown on GaAs(001), with thicknesses of 8.5 and 10nm, respectively. The mesofrequency switching dynamics have been investigated by ac magneto-optic Kerr effect magnetometry. Dynamic hysteresis loops have been measured along the four major in-plane crystallographic axes [100], [110], [010], and [11¯0] in each film in the sinusoidal applied field frequency range of 0.2–2kHz. The coercive field Hc for the CoFe film is 1.4–2.9 times larger than that for the Fe film, depending on the measurement axis, indicating a larger effective energy barrier to reversal. Examining the coercive field as a function of frequency Hc(f) it is found that the time scales for the domain nucleation and wall propagation are 3–10 times longer in the CoFe than in the Fe film. As previously shown in epitaxial Fe films, a local minimum in Hc(f) can occur at the crossover from the wall propagation-dominated to the nucleation-dominated dynamic regime, and here we find that it is more pronounced for the CoFe than for the Fe film, indicating a reduction in domain-wall pinning. We conclude that the magnitude of the effective energy barrier to reversal sets the time scale for the domain nucleation and wall propagation processes and determines the characteristics of Hc(f) for the two films.
Structural, optical, and electrical properties of AgIn5Te8
Authors: Sánchez A. , Meléndez L. , Castro J. , Hernández J. A. , Hernández E. , Durante Rincón C. A.
Published: February 2005

Ag In 5 Te 8 was prepared by direct fusion of the stoichiometric mixture of the elements in an evacuated quartz ampoule. The analysis of x-ray powder diffraction data showed the presence of one single phase with tetragonal structure. The lattice parameters a=6.212Å and c=12.456Å were refined by means of the program WINPLOTR. Congruent fusion at 698°C was observed by differential thermal analysis measurements performed on samples sealed in evacuated quartz ampoules. Transmittance measurements were used to determine the absorption coefficient α. Two absorption edges were observed, one indirect at 1.1eV and one direct at 1.28eV, obtained from a plot of (α×hν)1∕2 vs hν and (α×hν)2 vs hν, respectively. A six-probe configuration was used to measure the electrical resistivity and the Hall coefficient from 10to400K. The activation energies values, estimated at 1.1 and 1.27eV from Arrhenius plots of the resistivity and the Hall coefficient, respectively, agree with those obtained for the energy gaps by optical measurements.
Vacuum ultraviolet measurements on hydrogen resonance lines in the Maryland Centrifugal Experiment
Authors: Ghosh J. , Elton R. , Griem H. , Teodorescu C. , Case A. , Ellis R.
Published: February 2005

Extended spectroscopic measurements of hydrogen emission into the vacuum ultraviolet region on the Maryland Centrifugal Experiment [R. F. Ellis, A. B. Hassam, S. Messer, and B. R. Osborn, Phys. Plasmas 8, 2057 (2001)] indicate, from opacity on the Lyman series, ∼6% atomic hydrogen coexisting with protons, electrons, and carbon-impurity ions in a plasma region where the temperature is ∼15eV. An explanation is offered, based upon charge exchange of entering cold hydrogen atoms with plasma protons, followed by collisional excitation and radiative decay.
Uniform estimates on the velocity in Rayleigh–Bénard convection
Authors: Núñez Manuel
Published: February 2005

The kinetic energy of a fluid located between two plates at different temperatures is easily bounded by classical inequalities. However, experiments and numerical simulations indicate that when the convection is turbulent, the volume of the domains in which the speed is large, is rather small. This could imply that the maximum of the speed, in contrast with its quadratic mean, does not admit an a priori upper bound. It is proved that, provided the pressure remains bounded, a uniform estimate for the speed maximum does indeed exist, and that it depends on the maxima of certain ratios between temperature, pressure, and velocity.
Simulations of starting gas jets at low Mach numbers
Authors: Iglesias Immaculada , Vera Marcos , Sánchez Antonio L. , Liñán Amable
Published: February 2005

The starting jet produced by the impulsively started discharge of a submerged gas stream of constant velocity through a circular orifice in a plane wall is investigated by integrating numerically the axisymmetric Navier–Stokes equations for moderately large values of the jet Reynolds number. The analysis is restricted to low-Mach-number jets, for which the jet-to-ambient temperature ratio γ=Tj∕To emerges as the most relevant parameter. It is seen that the leading vortex approaches a quasisteady structure propagating at an almost constant velocity, which is larger for smaller values of γ. The action of the baroclinic torque in regions of nonuniform temperature leads to significant vorticity production, with a constant overall rate equal to that of an inviscid starting jet.
Reasons for obtaining an optical dielectric constant from the Poole–Frenkel conduction behavior of atomic-layer-deposited HfO2 films
Authors: Jeong Doo Seok , Park Hong Bae , Hwang Cheol Seong
Published: February 2005

The leakage current characteristics of a 16-nm-thick HfO2 film, grown by atomic-layer-deposition using HfCl4 as Hf precursor and O3 as oxidant, were investigated. The electron injection from the Pt top electrode to the HfO2 films was measured at various temperatures. The measured leakage current versus applied bias voltage curves showed the Poole–Frenkel conduction behavior in the high electric field region. However, the estimated dielectric constant from the Poole–Frenkel fitting corresponds to the dielectric constant of the optical frequency region. The quantum mechanical calculation of the electron transition from the metal electrode to the traps in the HfO2 film showed that the transition time was very short (10−14–10−16s) under the applied field. Therefore, the dielectric response of the HfO2 film to the electron conduction by Poole–Frenkel mechanism must be of the optical frequency under steady state current conduction.
Thin bismuth film as a template for pentacene growth
Authors: Sadowski J. T. , Nagao T. , Yaginuma S. , Fujikawa Y. , Al-Mahboob A. , Nakajima K. , Sakurai T. , Thayer G. E. , Tromp R. M.
Published: February 2005

Thin Bi(001) films grown by ultrahigh vacuum deposition on Si(111)-7×7 surfaces at room temperature, were annealed at ∼400K in order to improve their morphology by reducing the step density on the surface. Annealed, well-ordered Bi(001) films have been subsequently used as substrates for growth of pentacene (Pn). It has been determined using low-energy electron microscope that Pn nucleates on Bi(001) into a highly ordered, crystalline layer, with Pn molecules “standing up” on the Bi surface, and the (001) plane on the growth front. Moreover, the Pn layer is aligned with the Bi(001) surface having a “point-on-line” commensurate relationship with the substrate. The Pn∕Bi(001) film crystallizes in a bulk-like structure directly from the first Pn layer. Formation of the thin film phase reported for the Pn growth on SiO2 and other inert substrates was not observed in our experiments.
Excellent magnetocaloric properties of La0.7Ca0.3−xSrxMnO3(0.05⩽x⩽0.25) single crystals
Authors: Phan Manh-Huong , Yu Seong-Cho , Hur Nam Hwi
Published: February 2005

This letter reports on the superior magnetocaloric properties of La0.7Ca0.3−xSrxMnO3 (x=0.05, 0.10, 0.20, and 0.25) single crystals. Upon 50 kOe applied field, the magnetic entropy changes (ΔSM) reach values of ∼10.5, 7.45, 6.97, and 6.86J∕kgK for x=0.05, 0.10, 0.20, and 0.25 compositions, respectively. The large magnetic entropy changes have been found to occur around 300 K, thus allowing magnetic refrigeration at room temperature. Due to the absence of grains in the single crystals, the ΔSM distribution here is much more uniform than that of gadolinium and polycrystalline manganites, which is desirable for an Ericson-cycle magnetic refrigerator. The single crystals have the large magnetic entropy changes induced by low magnetic field change, which is beneficial for the household application of active magnetic refrigerant (AMR) materials. These results indicate that the present single crystals are excellent candidates as working materials for AMR.
Ultraviolet poling of pure fused silica by high-intensity femtosecond radiation
Authors: Corbari Costantino , Kazansky Peter G. , Slattery Stephen A. , Nikogosyan David N.
Published: February 2005

We demonstrate UV poling of a pure fused silica sample by applying to it an electric field of 200 kV/cm and irradiating it with high-intensity (∼40GW∕cm2) femtosecond (220 fs) laser pulses at 264 nm.
Anthrax toxins suppress T lymphocyte activation by disrupting antigen receptor signaling
Authors: Paccani Silvia Rossi , Tonello Fiorella , Ghittoni Raffaella , Natale Mariarita , Muraro Lucia , D'Elios Mario Milco , Tang Wei-Jen , Montecucco Cesare , Baldari Cosima T.
Published: February 2005

Anthrax is an infection caused by pathogenic strains of Bacillus anthracis, which secretes a three-component toxic complex consisting of protective antigen (PA), edema factor (EF), and lethal factor (LF). PA forms binary complexes with either LF or EF and mediates their entry into host cells. Although the initial phases of bacterial growth occur in the lymph node, the host fails to mount an effective immune response. Here, we show that LT and ET are potent suppressors of human T cell activation and proliferation triggered through the antigen receptor. Both LT and ET inhibit the mitogen-activated protein and stress kinase pathways, and both toxins inhibit activation of NFAT and AP-1, two transcription factors essential for cytokine gene expression. These data identify a novel strategy of immune evasion by B. anthracis, based on both effector subunits of the toxic complex, and targeted to a key cellular component of adaptive immunity.
Direct in vivo VH to JH rearrangement violating the 12/23 rule
Authors: Koralov Sergei B. , Novobrantseva Tatiana I. , Hochedlinger Konrad , Jaenisch Rudolf , Rajewsky Klaus
Published: February 2005

V(D)J recombination at the immunoglobulin heavy chain (IgH) locus follows the 12/23 rule to ensure the correct assembly of the variable region gene segments. Here, we report characterization of an in vivo model that allowed us to study recombination violating the 12/23 rule, namely a mouse strain lacking canonical D elements in its IgH locus. We demonstrate that VH to JH joining can support the generation of all B cell subsets. However, the process is inefficient in that B cells and antibodies derived from the DH-less allele are not detectable if the latter is combined with a wild-type IgH allele. There is no preferential usage of any particular VH gene family or JH element in VHJH junctions, indicating that 23/23-guided recombination is possible, but is a low frequency event at the IgH locus in vivo.
Dok-1 and Dok-2 are negative regulators of lipopolysaccharide-induced signaling
Authors: Shinohara Hisaaki , Inoue Akane , Toyama-Sorimachi Noriko , Nagai Yoshinori , Yasuda Tomoharu , Suzuki Hiromi , Horai Reiko , Iwakura Yoichiro , Yamamoto Tadashi , Karasuyama Hajime , Miyake Kensuke , Yamanashi Yuji
Published: February 2005

Endotoxin, a bacterial lipopolysaccharide (LPS), causes fatal septic shock via Toll-like receptor (TLR)4 on effector cells of innate immunity like macrophages, where it activates nuclear factor κB (NF-κB) and mitogen-activated protein (MAP) kinases to induce proinflammatory cytokines such as tumor necrosis factor (TNF)-α. Dok-1 and Dok-2 are adaptor proteins that negatively regulate Ras–Erk signaling downstream of protein tyrosine kinases (PTKs). Here, we demonstrate that LPS rapidly induced the tyrosine phosphorylation and adaptor function of these proteins. The stimulation with LPS of macrophages from mice lacking Dok-1 or Dok-2 induced elevated Erk activation, but not the other MAP kinases or NF-κB, resulting in hyperproduction of TNF-α and nitric oxide. Furthermore, the mutant mice showed hyperproduction of TNF-α and hypersensitivity to LPS. However, macrophages from these mutant mice reacted normally to other pathogenic molecules, CpG oligodeoxynucleotides, poly(I:C) ribonucleotides, or Pam3CSK4 lipopeptide, which activated cognate TLRs but induced no tyrosine phosphorylation of Dok-1 or Dok-2. Forced expression of either adaptor, but not a mutant having a Tyr/Phe substitution, in macrophages inhibited LPS-induced Erk activation and TNF-α production. Thus, Dok-1 and Dok-2 are essential negative regulators downstream of TLR4, implying a novel PTK-dependent pathway in innate immunity.
Bacterial toxins and the immune system
Authors: Galán Jorge E.
Published: February 2005

Microorganisms that cause persistent infection often exhibit specific adaptations that allow them to avoid the adaptive immune response. Recently, several bacterial toxins have been shown in vitro to disrupt immune cell functions. However, it remains to be established whether these activities are relevant during infection and whether these toxins have specifically evolved to disrupt the adaptive immune system.
Diversity within the Campylobacter jejuni type I restriction–modification loci
Authors: Miller William G. , Pearson Bruce M. , Wells Jerry M. , Parker Craig T. , Kapitonov Vladimir V. , Mandrell Robert E.
Published: February 2005

The type I restriction–modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA–H (R-linked ORF) and mloA–B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R–M systems are assigned to one of three families: ‘IAB’, ‘IC’ or ‘IF’. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The ‘IC’ hsd loci are >99 % identical at the nucleotide level, as are the ‘IF’ hsd loci. Additionally, whereas the nucleotide sequences of the ‘IAB’ hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the ‘IAB’ hsdS and rlo genes vary considerably. This diversity suggests that recombination between ‘IAB’ hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R–M systems is discussed.
Transcriptional profiling of Helicobacter pylori Fur- and iron-regulated gene expression
Authors: Ernst Florian D. , Bereswill Stefan , Waidner Barbara , Stoof Jeroen , Mäder Ulrike , Kusters Johannes G. , Kuipers Ernst J. , Kist Manfred , van Vliet Arnoud H. M. , Homuth Georg
Published: February 2005

Intracellular iron homeostasis is a necessity for almost all living organisms, since both iron restriction and iron overload can result in cell death. The ferric uptake regulator protein, Fur, controls iron homeostasis in most Gram-negative bacteria. In the human gastric pathogen Helicobacter pylori, Fur is thought to have acquired extra functions to compensate for the relative paucity of regulatory genes. To identify H. pylori genes regulated by iron and Fur, we used DNA array-based transcriptional profiling with RNA isolated from H. pylori 26695 wild-type and fur mutant cells grown in iron-restricted and iron-replete conditions. Sixteen genes encoding proteins involved in metal metabolism, nitrogen metabolism, motility, cell wall synthesis and cofactor synthesis displayed iron-dependent Fur-repressed expression. Conversely, 16 genes encoding proteins involved in iron storage, respiration, energy metabolism, chemotaxis, and oxygen scavenging displayed iron-induced Fur-dependent expression. Several Fur-regulated genes have been previously shown to be essential for acid resistance or gastric colonization in animal models, such as those encoding the hydrogenase and superoxide dismutase enzymes. Overall, there was a partial overlap between the sets of genes regulated by Fur and those previously identified as growth-phase, iron or acid regulated. Regulatory patterns were confirmed for five selected genes using Northern hybridization. In conclusion, H. pylori Fur is a versatile regulator involved in many pathways essential for gastric colonization. These findings further delineate the central role of Fur in regulating the unique capacity of H. pylori to colonize the human stomach.
Molecular characterization of the CmbR activator-binding site in the metC–cysK promoter region in Lactococcus lactis
Authors: Golic Natasa , Schliekelmann Martijn , Fernández María , Kleerebezem Michiel , van Kranenburg Richard
Published: February 2005

ThemetC–cysKoperon involved in sulphur metabolism inLactococcus lactisis positively regulated by the LysR-type protein CmbR. Transcription from themetCpromoter is activated when concentrations of methionine and cysteine in the growth medium are low. ThemetCpromoter region contains two direct and three inverted repeats. Deletion analysis indicated that direct repeat 2 (DR2) is required for activation of themetCpromoter by CmbR. Gel mobility shift assays confirmed that CmbR binds to a 407 bp DNA fragment containing themetCpromoter. This binding was stimulated byO-acetyl-l-serine. Competition experiments with deletion variants of themetCpromoter showed that CmbR binding only occurred with fragments containing an intact DR2, confirming that DR2 is the CmbR binding site within themetCpromoter.
A new subfamily of fungal subtilases: structural and functional analysis of a Pleurotus ostreatus member
Authors: Faraco Vincenza , Palmieri Gianna , Festa Giovanna , Monti Maria , Sannia Giovanni , Giardina Paola
Published: February 2005

Pleurotus ostreatus produces several extracellular proteases which are believed to be involved in the regulation of the ligninolytic activities of this fungus. Recently, purification and characterization of the most abundant P. ostreatus extracellular protease (PoSl) have been reported. The sequence of the posl gene and of the corresponding cDNA has been determined, allowing the identification of its pre- and pro-sequences. A mature protein sequence has been verified by mass spectrometry mapping, the N-glycosylation sites have been identified and the glycosidic moieties characterized. Mature PoSl shows a cleaved peptide bond in the C-terminal region, which remains associated with the catalytic domain in a non-covalent complex. Reported results indicate that this enzyme is involved in the activation of other P. ostreatus secreted proteases, thus suggesting its leading role in cascade activation mechanisms. Analyses of the PoSl sequence by homology search resulted in the identification of a DNA sequence encoding a new protease, homologous to PoSl, in the Phanerochaete chrysosporium genome. A new subgroup of subtilisin-like proteases, belonging to the pyrolysin family, has been defined, which includes proteases from ascomycete and basidiomycete fungi.
Point mutations in the DNA- and cNMP-binding domains of the homologue of the cAMP receptor protein (CRP) in Mycobacterium bovis BCG: implications for the inactivation of a global regulator and strain attenuation
Authors: Spreadbury Claire L. , Pallen Mark J. , Overton Tim , Behr Marcel A. , Mostowy Serge , Spiro Stephen , Busby Stephen J. W. , Cole Jeffrey A.
Published: February 2005

The genome of Mycobacterium tuberculosis H37Rv includes a homologue of the CRP/FNR (cAMP receptor protein/fumarate and nitrate reduction regulator) family of transcription regulators encoded by Rv3676. Sequencing of the orthologous gene from attenuated Mycobacterium bovis Bacille Calmette–Guérin (BCG) strains revealed point mutations that affect the putative DNA-binding and cNMP-binding domains of the encoded protein. These mutations are not present in the published sequences of the Rv3676 orthologues in M. bovis, M. tuberculosis or Mycobacterium leprae. An Escherichia coli lacZ reporter system was used to show that the M. tuberculosis Rv3676 protein binds to DNA sites for CRP, but this DNA binding was decreased or abolished with the Rv3676 protein counterparts from BCG strains. The DNA-binding ability of the M. tuberculosis Rv3676 protein was decreased by the introduction of base changes corresponding to the BCG point mutations. Conversely, the DNA binding of the BCG Rv3676 proteins from BCG strains was restored by removing the mutations. These data show that in this reporter system the point mutations present in the Rv3676 orthologue in BCG strains render its function defective (early strains) or abolished (late strains) and suggest that this protein might be naturally defective in M. bovis BCG strains. This raises the possibility that a contributing factor to the attenuation of BCG strains may be an inability of this global regulator to control the expression of genes required for in vivo survival and persistence.
Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis
Authors: Steil Leif , Serrano Mónica , Henriques Adriano O. , Völker Uwe
Published: February 2005

Temporal and compartment-specific control of gene expression during sporulation inBacillus subtilisis governed by a cascade of four RNA polymerase subunits.σFin the prespore andσEin the mother cell control early stages of development, and are replaced at later stages byσGandσK, respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and abofAallele, which allowsσKactivation in the absence ofσG. As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in theσFregulon, 154σE-governed genes, 113σG-dependent genes, and 132 genes underσKcontrol. The results strengthen the view that the activities ofσF,σE,σGandσKare largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (σA) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.
Virulence attenuation in Salmonella enterica rcsC mutants with constitutive activation of the Rcs system
Authors: García-Calderón Clara B. , García-Quintanilla Meritxell , Casadesús Josep , Ramos-Morales Francisco
Published: February 2005

Mutations inrcsCthat result in constitutive colanic acid capsule synthesis were obtained inSalmonella entericaserovar Typhimurium. MostrcsCalleles were dominant; however, recessivercsCalleles were also found, in agreement with the postulated double role (positive and negative) of RcsC on the activation of the RcsB/C phosphorelay system.Salmonella rcsCmutants with constitutive activation of the Rcs system are severely attenuated for virulence in BALB/c mice and their degree of attenuation correlates with the level of Rcs activation. Partial relief of attenuation by agmmmutation indicates that capsule overproduction is one of the factors leading to avirulence in constitutively activatedrcsCmutants.
Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate
Authors: Overhage Jörg , Sielker Sonja , Homburg Stefan , Parschat Katja , Fetzner Susanne
Published: February 2005

Arthrobacter nitroguajacolicusRü61a, which utilizes quinaldine as sole source of carbon and energy, was shown to contain a conjugative linear plasmid of approximately 110 kb, named pAL1. It exhibits similarities with other linear plasmids fromActinomycetalesin that it has proteins covalently attached to its 5′ ends. Southern hybridization with probes for the genes encoding quinaldine 4-oxidase andN-acetylanthranilate amidase indicated that pAL1 contains the gene cluster encoding the degradation of quinaldine to anthranilate. A mutant of strain Rü61a that had lost pAL1 indeed could not convert quinaldine, but was still able to grow on anthranilate. Conjugative transfer of pAL1 to the plasmid-less mutant of strain Rü61a and toArthrobacter nicotinovoransDSM 420 (pAO1) occurred at frequencies of 5·4×10−4and 2·0×10−4per recipient, respectively, and conferred the ability to utilize quinaldine. Five other quinaldine-degrading Gram-positive strains were isolated from soil samples; 16S rDNA sequence analysis suggested the closest relationship to differentArthrobacterspecies. Except for strain K2-29, all isolates contained a pAL1-like linear plasmid carrying genes encoding quinaldine conversion. A 478 bp fragment that on pAL1 represents an intergenic region showed 100 % sequence identity in all isolates harbouring a pAL1-like plasmid, suggesting horizontal dissemination of the linear plasmid among the genusArthrobacter.
DNA base excision repair potentiates the protective effect of Salmonella Pathogenicity Island 2 within macrophages
Authors: Suvarnapunya Akamol E. , Stein Murry A.
Published: February 2005

Reactive oxidants are a primary weapon of the macrophage antibacterial arsenal. The ability of virulentSalmonellato repair oxidative DNA lesions via the base-excision repair system (BER) enables its survival and replication within the macrophage, but is not required for extracellular growth.Salmonellaalso inhibits the targeting of oxidant generators to theSalmonella-containing vacuole (SCV) viaSalmonellaPathogenicity Island 2 (SPI2). Accordingly, the relative contributions of these two discrete systems toSalmonellaresistance to both oxidative mutagenesis and lethality within RAW 264.7 macrophages were investigated. A mutant unable to initiate BER was constructed by deleting all three BER bifunctional glycosylases (Δfpg/nth/nei), and was significantly impaired for early intramacrophage survival. Mutations in various SPI2 effector (sifAandsseEFG) and structural (ssaV) genes were then analysed in the BER mutant background. Loss of SPI2 function alone appeared to increase macrophage-induced mutation. Statistical analyses of the reduced intramacrophage survival of SPI2 mutants and the corresponding SPI2/BER mutants indicated a synergistic interaction between BER and SPI2, suggesting that SPI2 promotes intramacrophage survival by protectingSalmonellaDNA from exposure to macrophage oxidants. Furthermore, this protection may involve the SseF and SseG effectors. In contrast, the SifA effector did not seem to play a major role in oxidant protection. It is speculated thatSalmonellainitially stalls oxidative killing by preserving its genomic integrity through the function of BER, until it can upregulate SPI2 to limit its exposure to macrophage oxidants.
The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm
Authors: Arnvig Kristine B. , Gopal B. , Papavinasasundaram K. G. , Cox Robert A. , Colston M. Joseph
Published: February 2005

Mycobacteria are slow-growing bacteria with a generation time of from 2–3 h up to several weeks. Consistent with the low growth rate, mycobacterial species have a maximum of two rRNA operons, rrnA and rrnB. The rrnA operon is present in all mycobacteria and has between two and five promoters, depending on species, whereas the rrnB operon, with a single promoter, is only found in some of the faster-growing species. The promoter region of the rrnB operon of a typical fast grower, Mycobacterium smegmatis, was investigated. By using lacZ reporter gene fusions it was demonstrated that the rrnB operon contains a highly activating region upstream of the core promoter, comparable to other bacterial rrn operons. However, the results suggest that, unlike the situation in, for example, Escherichia coli, the activating mechanism is solely factor dependent, and that no UP element is involved.
Analysis of type IV pilus and its associated motility in Myxococcus xanthus using an antibody reactive with native pilin and pili
Authors: Li Yinuo , Lux Renate , Pelling Andrew E. , Gimzewski James K. , Shi Wenyuan
Published: February 2005

Myxococcus xanthus possesses a social gliding motility that requires type IV pili (TFP). According to the current model, M. xanthus pili attach to an external substrate and retract, pulling the cell body forward along their long axis. By analogy with the situation in other bacteria employing TFP-dependent motility, M. xanthus pili have been assumed to be composed of pilin (PilA) subunits, but this has not previously been confirmed. The first 28 amino acids of the M. xanthus PilA protein share extensive homology with the N-terminal oligomerization domain of pilins in other bacterial species. To facilitate purification, the authors engineered a truncated form of M. xanthus PilA lacking the first 28 amino acids and purified this protein in soluble form. Polyclonal antibody generated against this protein was reactive with native pilin and pili. Using this antibody, it was confirmed that TFP of M. xanthus are indeed composed of PilA, and that TFP are located unipolarly and required for social gliding motility via retraction. Using tethering as well as motility assays, details of pili function in M. xanthus social motility were further examined.
Genetic analysis of the β-lactamases of Mycobacterium tuberculosis and Mycobacterium smegmatis and susceptibility to β-lactam antibiotics
Authors: Flores Anthony R. , Parsons Linda M. , Pavelka, Martin S.
Published: February 2005

Mycobacteria produce β-lactamases and are intrinsically resistant to β-lactam antibiotics. In addition to the β-lactamases, cell envelope permeability and variations in certain peptidoglycan biosynthetic enzymes are believed to contribute to β-lactam resistance in these organisms. To allow the study of these additional mechanisms, mutants of the major β-lactamases, BlaC and BlaS, were generated in the pathogenic Mycobacterium tuberculosis strain H37Rv and the model organism Mycobacterium smegmatis strain PM274. The mutants M. tuberculosis PM638 (ΔblaC1) and M. smegmatis PM759 (ΔblaS1) showed an increase in susceptibility to β-lactam antibiotics, as determined by disc diffusion and minimal inhibitory concentration (MIC) assays. The susceptibility of the mutants, as assayed by disc diffusion tests, to penicillin-type β-lactam antibiotics was affected most, compared to the cephalosporin-type β-lactam antibiotics. The M. tuberculosis mutant had no detectable β-lactamase activity, while the M. smegmatis mutant had a residual type 1 β-lactamase activity. We identified a gene, blaE, encoding a putative cephalosporinase in M. smegmatis. A double β-lactamase mutant of M. smegmatis, PM976 (ΔblaS1ΔblaE : : res), had no detectable β-lactamase activity, but its susceptibility to β-lactam antibiotics was not significantly different from that of the ΔblaS1 parental strain, PM759. The mutants generated in this study will help determine the contribution of other β-lactam resistance mechanisms in addition to serving as tools to study the biology of peptidoglycan biosynthesis in these organisms.
A Syntactic Bias in Scope Ambiguity Resolution in the Processing of English‐French Cardinality Interrogatives: Evidence for Informational Encapsulation
Authors: Dekydtspotter Laurent , Outcalt Samantha D.
Published: February 2005

This article presents a reading‐time study of scope resolution in the interpretation of ambiguous cardinality interrogatives in English‐French and in English and French native sentence processing. Participants were presented with a context, a self‐paced segment‐by‐segment presentation of a cardinality interrogative, and a numerical answer that respondents either accepted or rejected. Very narrowly distributed and interpretation‐dependent reading‐time asymmetries arose in English‐French processing and in French and English native processing. A syntactic account of scope resolution characterizes the reading‐time asymmetries produced by English‐French learners and differences between French and English native respondents. In contrast, a context‐driven theory of scope resolution encounters many severe problems that render its plausibility exceedingly remote.
Testing the Effects of Regional, Ethnic, and International Dialects of English on Listening Comprehension
Authors: Major Roy C. , Fitzmaurice Susan M. , Bunta Ferenc , Balasubramanian Chandrika
Published: February 2005

It is widely believed that listeners understand some dialects more easily than others, although there is very little research that has rigorously measured the effects. This study investigated whether listeners experience more difficulty with regional, ethnic, and international dialects of English than with Standard American English. The results demonstrated that speaker dialect had a significant effect for both English as a second language (ESL) listeners (n = 158) and native‐English‐speaking listeners (n = 58). ESL listeners scored lower on listening comprehension tests hearing ethnic and international dialects of English compared to Standard American English; however, there were no significant differences between the scores of those hearing regional dialect and Standard American English. These results suggest that regional dialects should be considered in listening comprehension tests such as the Test of English as a Foreign Language.
Firm Size Dependence in the Determinants of Bank Term Loan Maturity
Authors: Dennis Steven A. , Sharpe Ian G.
Published: February 2005

Abstract:  We examine the hypothesis that firm size affects the sensitivity of bank term loan maturity to its underlying determinants. As borrower size increases, negotiating power with the lender and information transparency increase, while the lender is able to spread the fixed costs of loan production across a larger dollar value of the loan. We find strong evidence of firm size dependency in the determinants of bank term loan maturity and show that this is unrelated to syndication. Only large borrowers can manipulate bank loan contract terms so as to increase firm value.
Top Director Shake‐up: The Link between Chairman and CEO Dismissal in the UK
Authors: Florou Annita
Published: February 2005

Abstract:  Most UK companies separate the roles of CEO and Chairman. The former runs the company and the latter runs the board. Using turnover data on 2,180 separate Chairmanships of the top 460 UK firms over the 1990–1998 period, I find that the Chairman is more likely to be replaced when the CEO is dismissed. Detailed data on the dismissal events suggests that Chairman replacement is associated with board restructuring. This may be necessary to bring in different skills and experience which, in turn, might facilitate changes in future corporate decisions. Moreover, I find that the Chairman's previous position, or the type of Chairmanship, does not affect the association between Chairman removal and CEO dismissal. But, the increase in the dismissal likelihood of the Chairman at the time of forced CEO departure is higher when she is involved in the appointment of the failing CEO. This, in turn, can be interpreted as an indication of effective governance.
US, UK and European Stock Market Integration
Authors: Fraser Patricia , Oyefeso Oluwatobi
Published: February 2005

Abstract:  This paper examines long‐run convergence between US, UK and seven European stock markets. We report evidence to suggest that while real short‐run diversification gains may occur, in general they tend to be short‐lived. However we also find that US and UK markets are relatively less bound to a common trend, which would imply that increased stock market merger activity, and any transition to the European common currency by the UK, may lead to relatively large stock market adjustments as markets adapt to these institutional changes.
Futures Trading Activity and Commodity Cash Price Volatility
Authors: Yang Jian , Balyeat R. Brian , Leatham David J.
Published: February 2005

Abstract:  This paper examines the lead‐lag relationship between futures trading activity (volume and open interest) and cash price volatility for major agricultural commodities. Granger causality tests and generalized forecast error variance decompositions show that an unexpected increase in futures trading volume unidirectionally causes an increase in cash price volatility for most commodities. Likewise, there is a weak causal feedback between open interest and cash price volatility. These findings are generally consistent with the destabilizing effect of futures trading on agricultural commodity markets.
The Wealth and Risk Effects of the Gramm‐Leach‐Bliley Act (GLBA) on the US Banking Industry
Authors: Mamun Abdullah , Hassan M. Kabir , Maroney Neal
Published: February 2005

Abstract:  The Gramm‐Leach‐Bliley Act (GLBA) of 1999 marks the end of Depression era regulations like the Glass‐Steagall Act of 1933 and Bank Holding Company Act of 1956. These acts have restricted banks from securities and insurance underwriting business. This paper examines the impact of the GLBA on the banking industry. We find that the banking industry has a welfare gain from this law. We investigate two different categorizations of the banking industry. We find that Money Center banks followed by the Super Regional banks benefited most from this deregulation. On the other hand, banks that had Section 20 investment subsidiaries gained more than other banks in the second category. The results also show that the exposure to systematic risk for different categories of banks decreased after the passage of this law, which implies that the GLBA is fairly successful in containing the risk that accompanied the act and also created diversification opportunities. For Money Center banks, Super Regional Banks, banks with a section 20 subsidiary and banks with a new financial subsidiary, a shift in the exposure to systematic risk can explain the overall cross sectional variation in return from the deregulation. In both categorizations we find that larger banks gained more, while the overall explanatory power of profitability is not conclusive.
The Role of Private Knowledge in Reducing the Information Wedge: A Research Note
Authors: Hanley Aoife , Crook Jonathan
Published: February 2005

Abstract:  In this first ever study to examine the marginal importance of collateral level vis‐à‐vis reputation in reducing information asymmetry, we find using unique data for UK business credit, that pre‐existing reputation is the single‐most important determinant in inducing a bank to extend a loan. Moreover, a bank responds positively to higher levels of collateral and negatively to higher credit requests. Similar to Cole (1998), but controlling for collateral level, we find that it helps to have banked with the lender before. Non‐trivial information search costs imply an important role for reputation in extending credits.
The lobular expression of the rat asialoglycoprotein receptor is regulated at the posttranscriptional level
Authors: Massimi Mara , Leoni Silvia , Devirgiliis Laura Conti
Published: February 2005

Abstract: The purpose of this study was to define the distribution of the asialoglycoprotein receptor (ASGP‐R) main peptide, rat hepatic lectin (RHL)‐1, within the rat liver lobule and to investigate its possible modulation in physiological states characterised by marked changes of receptorial expression. In particular, we chose livers from rats partially hepatectomised or at the end of pregnancy, as models, respectively, of decreased or increased expression of the ASGP‐R, and used the in situ hybridisation and immunocytochemistry techniques to analyse in parallel the lobular distributions of RHL‐1 mRNA and protein. In normal rat liver, although the RHL‐1 mRNA was homogeneously distributed, the RHL‐1 peptide was predominantly localised on the surface of pericentral hepatocytes with a gradient of expression towards the periportal zone. This gradient of expression of RHL‐1 peptide was reduced in regenerating livers, in which the positive stain was restricted to a few layers of cells around the central vein. In contrast, livers at the end of pregnancy showed an overall increase of the peptide with a concomitant flattening of the gradient across the liver plate. In all the conditions, we never observed important changes in the pattern of expression of the specific mRNA. These findings indicate that the distribution of ASGP‐R is heterogeneous across the liver lobule, with a pattern of expression prevalently modulated at the posttranscriptional level.
Mutations of β‐catenin and AXIN I genes are a late event in human hepatocellular carcinogenesis
Authors: Park Jik Young , Park Won Sang , Nam Suk Woo , Kim Su Young , Lee Sug Hyung , Yoo Nam Jin , Lee Jung Young , Park Cheol Keun
Published: February 2005

Abstract: Background: Hepatocellular carcinoma (HCC) is a well‐known cancer involving the Wnt pathway in its carcinogenesis.

Aims: However, it is not clear whether these genetic changes are early genetic events in hepatocarcinogenesis or not.

Method: In this study, we performed mutational analysis of the β‐catenin and AXIN I genes, and immunohistochemistry for β‐catenin in a series of 114 hepatocellular nodular lesions, including premalignant lesions such as low‐grade dysplastic nodules (LGDNs) and high‐grade dysplastic nodules (HGDNs). Results: In the present study, mutations of the β‐catenin and AXIN I genes were detected in 16% (13 out of 81) and 6.2% (five of 81) of the HCCs, respectively. However, no mutations were found in 14 LGDNs and 19 HGDNs. Moreover, abnormal nuclear β‐catenin immunostaining was observed in 30 of 81 HCCs, but not in dysplastic nodules.

Conclusion: Taken together, our data suggest that β‐catenin stabilization because of either β‐catenin or AXIN I mutation might be a late event for malignant progression rather than an early genetic event involving the initiation of HCC development.