bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Downstream Passage on the Flow Within an Annular S-Shaped Duct
Authors: Sonoda T. , Arima T. , Oana M.
Published: December 2008

Experimental and numerical investigations were carried out to gain a better understanding of the flow characteristics within an annular S-shaped duct, including the influence of the shape of the downstream passage located at the exit of the duct on the flow. A duct with six struts and the same geometry as that used to connect the compressor spools on our new experimental small two-spool turbofan engine was investigated. Two types of downstream passage were used. One type had a straight annular passage and the other a curved annular passage with a meridional flow path geometry similar to that of the centrifugal compressor. Results showed that the total pressure loss near the hub is large due to instability of the flow, as compared with that near the casing. Also, a vortex related to the horseshoe vortex was observed near the casing. In the case of the curved annular passage, the total pressure loss near the hub was greatly increased compared with the case of the straight annular passage, and the spatial position of this vortex depends on the passage core pressure gradient. Furthermore, results of calculation using an in-house-developed three-dimensional Navier–Stokes code with a low-Reynolds-number k–ε turbulence model were in good qualitative agreement with experimental results. According to the simulation results, a region of very high pressure loss is observed near the hub at the duct exit with the increase of inlet boundary layer thickness. Such regions of high pressure loss may act on the downstream compressor as a large inlet distortion, and strongly affect downstream compressor performance.
An Analysis Method for Multistage Transonic Turbines With Coolant Mass Flow Addition
Authors: Mildner F. , Gallus H. E.
Published: December 2008

The subject of this paper is a numerical method for the calculation of the transonic flow field of multistage turbines, taking high coolant flow into account. To reduce the processing time, a throughflow method based on the principels of Wu is used for the hub-to-tip calculation. The flow field is obtained by an iterative solution between a three-dimensional inviscid hyperbolic time-dependent algorithm with an implicit finite volume method for the blade-to-blade calculations using C-meshes and a single representative meridional S2m-streamsurface. Along the S2m-plane with respect to nonorthogonal curvilinear coordinates, the stream function equation governing fluid flow is established. The cooling air inflow inside the blade passage forbids the assumption of a constant mass flow along the main stream direction. To consider the change of the aerodynamic and thermodynamic behavior, a cooling air model was developed and implemented in the algorithm, which allows the mixing of radially arbitrarily distributed cooling air in the trailing edge section of each blade row. The viscous effects and the influence of cooling air mixing are considered by the use of selected loss correlations for profile, tip leakage, secondary flow and mixing losses in the S2m-plane in terms of entropy. The method is applied to the four-stage high-temperature gas turbine Siemens KWU V84.3. The numerical results obtained are in good agreement with the experimental data.
Aspects of Vane Film Cooling With High Turbulence: Part I—Heat Transfer
Authors: Ames F. E.
Published: December 2008

A four-vane subsonic cascade was used to investigate the influence of film injection on vane heat transfer distributions in the presence of high turbulence. The influence of high turbulence on vane film cooling effectiveness and boundary layer development was also examined in part II of this paper. A high-level, large-scale inlet turbulence was generated for this study with a mock combustor (12 percent) and was used to contrast results with a low level (1 percent) of inlet turbulence. The three geometries chosen to study in this investigation were one row and two staggered rows of downstream cooling was found to have only a moderate influence on the heat transfer coefficients downstream from arrays on the suction surface where the boundary layer was turbulent. However, film cooling was found to have a substantial influence on heat transfer downstream from arrays in laminar regions of the vane such as the pressure surface, the stagnation region, and the near-suction surface. Generally, heat transfer augmentation was found to scale on velocity ratio. In relative terms, the augmentation in the laminar regions for the low turbulence case was found to be the highest for the high turbulence case.
Aspects of Vane Film Cooling With High Turbulence: Part II—Adiabatic Effectiveness
Authors: Ames F. E.
Published: December 2008

A four-vane subsonic cascade was used to investigate the influence of turbulence on vane film cooling distributions. The influence of film injection on vane heat transfer distributions in the presence of high turbulence was examined in part I of this paper. Vane effectiveness distributions were documented in the presence of a low level of turbulence (1 percent) and were used to contrast results taken at a high level (12 percent) of large-scale turbulence. All data were taken at a density ratio of about 1. The three geometries chosen to study included one row and two staggered rows of downstream film cooling on both the suction and pressure surfaces as well as a showerhead array. Turbulence was found to have a moderate influence on pressure surface film cooling, particularly at the lower velocity ratios. The strong pressure gradients on the pressure surface of the vane were also found to alter film cooling distributions substantially. At lower velocity ratios, effectiveness distributions for two staggered rows of holes could be predicted well using data from one row superposed. At higher velocity ratios the two staggered rows produced significantly higher levels of effectiveness than values estimated from single row data superposed. Turbulence was also found to reduce effectiveness levels produced by showerhead film cooling substantially.
Effect of Unsteady Wake on Detailed Heat Transfer Coefficient and Film Effectiveness Distributions for a Gas Turbine Blade
Authors: Du H. , Han J. C. , Ekkad S. V.
Published: December 2008

Unsteady wake effects on detailed heat transfer coefficient and film cooling effectiveness distributions from a gas turbine blade with film cooling are obtained using a transient liquid crystal technique. Tests were performed on a five-blade linear cascade at a axial chord Reynolds number of 5.3 × 105 at cascade exit. Upstream unsteady wakes are simulated using a spoke-wheel type wake generator. The test blade has three rows of film holes on the leading edge and two rows each on the pressure and suction surfaces. Air and CO2 were used as coolants to simulate different coolant-to-mainstream density ratio effect. Coolant blowing ratio for air injection is varied from 0.8 to 1.2 and is varied from 0.4 to 1.2 for CO2. Results show that Nusselt numbers for a film-cooled blade are much higher compared to a blade without film injection. Particularly, film injection causes earlier boundary layer transition on the suction surface. Unsteady wakes slightly enhance Nusselt numbers but significantly reduce film cooling effectiveness on a film-cooled blade compared with a film-cooled blade without wakes. Nusselt numbers increase slightly but film cooling effectiveness increase significantly with an increase in blowing ratio for CO2 injection. Higher density coolant (CO2) provides higher effectiveness at higher blowing ratios (M = 1.2) whereas lower density coolant (Air) provides higher effectiveness at lower blowing ratios (M = 0.8).
The Effect of Turbulence on the Heat Transfer in Closed Gas-Filled Rotating Annuli
Authors: Bohn D. , Gier J.
Published: December 2008

Higher turbine inlet temperatures are a common measure for increasing the thermal efficiency of modern gas turbines. This development leads not only to the need for more efficient turbine blade cooling but also to the requirement for a more profound knowledge of the mechanically and thermally stressed parts of the rotor. For determining thermal stresses from the temperature distribution in the rotor of a gas turbine, one has to encounter the convective transfer in rotor cavities. In the special case of an entirely closed gas-filled rotating annulus, the convective flow is governed by a strong natural convection. Owen and other researchers have found that the presence of turbulence and its inclusion in the modeling of the flow causes significant differences in the flow development in rotating annuli with throughflow, e.g., different vortex structures. However, in closed rotating annuli there is still a lack of knowledge concerning the influence of turbulence. Based on previous work, in this paper the influence of turbulence on the flow structure and on the heat transfer is investigated. The flow is investigated numerically with a three-dimensional Navier–Stokes solver, based on a pressure correction scheme. To account for the turbulence, a low-Reynolds-number k–ε model is employed. The results are compared with experiments performed at the Institute of Steam and Gas Turbines. The computations demonstrate that turbulence has a considerable influence on the overall heat transfer as well as on the local heat transfer distribution. Three-dimensional effects are discussed by comparing the three-dimensional calculation with a two-dimensional calculation of the same configuration and are found to have some impact.
A Dynamic Marine Calcium Cycle During the Past 28 Million Years
Authors: Griffith Elizabeth M. , Paytan Adina , Caldeira Ken , Bullen Thomas D. , Thomas Ellen
Published: December 2008

Multiple lines of evidence have shown that the isotopic composition and concentration of calcium in seawater have changed over the past 28 million years. A high-resolution, continuous seawater calcium isotope ratio curve from marine (pelagic) barite reveals distinct features in the evolution of the seawater calcium isotopic ratio suggesting changes in seawater calcium concentrations. The most pronounced increase in the δ
44/40
Ca value of seawater (of 0.3 per mil) occurred over roughly 4 million years following a period of low values around 13 million years ago. The major change in marine calcium corresponds to a climatic transition and global change in the carbon cycle and suggests a reorganization of the global biogeochemical system.
Compromised Survivorship in Zoo Elephants
Authors: Clubb Ros , Rowcliffe Marcus , Lee Phyllis , Mar Khyne U. , Moss Cynthia , Mason Georgia J.
Published: December 2008

We analyzed data from over 4500 elephants to show that animals in European zoos have about half the median life span of conspecifics in protected populations in range countries. This discrepancy is clearest in Asian elephants; unlike African elephants in zoos, this species' infant mortality is very high (for example, twice that seen in Burmese timber camps), and its adult survivorship in zoos has not improved significantly in recent years. One risk factor for Asian zoo elephants is being moved between institutions, with early removal from the mother tending to have additional adverse effects. Another risk factor is being born into a zoo rather than being imported from the wild, with poor adult survivorship in zoo-born Asians apparently being conferred prenatally or in early infancy. We suggest stress and/or obesity as likely causes of zoo elephants' compromised survivorship.
A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation
Authors: Singh Satinder K. , Piscitelli Chayne L. , Yamashita Atsuko , Gouaux Eric
Published: December 2008

Secondary transporters are workhorses of cellular membranes, catalyzing the movement of small molecules and ions across the bilayer and coupling substrate passage to ion gradients. However, the conformational changes that accompany substrate transport, the mechanism by which a substrate moves through the transporter, and principles of competitive inhibition remain unclear. We used crystallographic and functional studies on the leucine transporter (LeuT), a model for neurotransmitter sodium symporters, to show that various amino acid substrates induce the same occluded conformational state and that a competitive inhibitor, tryptophan (Trp), traps LeuT in an open-to-out conformation. In the Trp complex, the extracellular gate residues arginine 30 and aspartic acid 404 define a second weak binding site for substrates or inhibitors as they permeate from the extracellular solution to the primary substrate site, which demonstrates how residues that participate in gating also mediate permeation.
Roles of NF-κB Activation and Peroxisome Proliferator-Activated Receptor Gamma Inhibition in the Effect of Rifampin on Inducible Nitric Oxide Synthase Transcription in Human Lung Epithelial Cells
Authors: Yuhas Yael , Berent Eva , Cohen Regev , Ashkenazi Shai
Published: December 2008

Rifampin (rifampicin), an important antibiotic agent and a major drug used for the treatment of tuberculosis, exerts immunomodulatory effects. Previous studies have found that rifampin increases inducible nitric oxide (NO) synthase (iNOS) expression and NO production. The present study investigated the potential mechanism(s) underlying these actions. The incubation of human lung epithelial A549 cells with a cytokine mix (interleukin-1β, tumor necrosis factor alpha, and gamma interferon) induced the expression of iNOS mRNA. The addition of rifampin increased the iNOS level by 1.9 ± 0.3-fold at a dose of 10 μg/ml (
P
< 0.01) and by 4.0 ± 0.3-fold at a dose of 50 μg/ml (
P
< 0.001). Rifampin treatment also affected the transcription factors that regulate iNOS mRNA: there was an increased and prolonged degradation of the inhibitory subunit of NF-κB, a corresponding increase in the level of cytokine-induced DNA binding of NF-κB (2.1 ± 0.2-fold), and a decrease in the level of expression of peroxisome proliferator-activated receptor gamma (PPARγ). Specifically, the level of PPARγ expression dropped by 15% in response to cytokine stimulation and by an additional 40% when rifampin was added (
P
< 0.001). Rifampin had no effect on the activation of mitogen-activated protein kinases or the signal transducer and transcription activator (STAT-1). In conclusion, rifampin augments NO production by upregulating iNOS mRNA. It also increases the level of NF-κB activation and decreases the level of PPARγ expression. The increases in the levels of NF-κB activation and NO production probably contribute to the therapeutic effects of rifampin. However, given the role of NF-κB in upregulating many inflammatory genes and the roles of PPARγ in downregulating inflammatory genes and in lipid and glucose metabolism, these findings have implications for potential adverse effects of rifampin in patients with chronic inflammatory diseases and glucose or lipid disorders.
Pharmacokinetics and Safety of Caspofungin in Older Infants and Toddlers
Authors: Neely Michael , Jafri Hasan S. , Seibel Nita , Knapp Katherine , Adamson Peter C. , Bradshaw Susan K. , Strohmaier Kim M. , Sun Peng , Bi Sheng , Dockendorf Marissa Fallon , Stone Julie A. , Kartsonis Nicholas A.
Published: December 2008

Although information about the efficacy and safety experience with caspofungin at 50 mg/m
2
daily is available for children and adolescents, the dosing regimen in infants and toddlers 3 to 24 months of age has yet to be established. We studied the pharmacokinetics and safety of caspofungin at 50 mg/m
2
once daily in nine patients 10 to 22 months (median, 13 months) of age with fever and neutropenia who received caspofungin once daily for 2 to 21 (mean, 9.3) days. Plasma caspofungin concentrations were measured by high-performance liquid chromatography assay on days 1 and 4. On day 4, the area under the curve from 0 to 24 h (AUC
0-24
) was 130.3 μg-h/ml, the peak concentration (
C
1
) was 17.2 μg/ml, and the trough concentration (
C
24
) was 1.6 μg/ml. The day 4 geometric mean ratios (GMRs) and 90% confidence interval (CI) for these parameters in infants/toddlers relative to adults were 1.26 (1.06, 1.50), 1.83 (1.57, 2.14), and 0.81 (0.64, 1.04), respectively. Relative to children (2 to 11 years of age), the day 4 GMRs (and 90% CI) were 1.13 (0.89, 1.44), 1.10 (0.85, 1.42), and 1.12 (0.72, 1.76), respectively. The harmonic mean elimination phase
t
1/2
in infants/toddlers (8.8 h) was reduced ∼33% relative to adults (13.0 h) but was similar to that in children (8.2 h). Clinical adverse events occurred in seven patients (78%); none were considered drug related. Laboratory adverse events occurred in five patients (56%) and were considered drug related in three (33%). There were no infusion-related events or discontinuations due to toxicity. Caspofungin at 50 mg/m
2
daily was well tolerated in infants and toddlers; the AUC and caspofungin
C
24
were generally comparable to those in adults receiving caspofungin at 50 mg daily.
Fermentation of Barley by Using
Saccharomyces cerevisiae
: Examination of Barley as a Feedstock for Bioethanol Production and Value-Added Products
Authors: Gibreel Amera , Sandercock James R. , Lan Jingui , Goonewardene Laksiri A. , Zijlstra Ruurd T. , Curtis Jonathan M. , Bressler David C.
Published: December 2008

The objective of this study was to examine the ethanol yield potential of three barley varieties (Xena, Bold, and Fibar) in comparison to two benchmarks, corn and wheat. Very high gravity (VHG; 30% solids) fermentations using both conventional and Stargen 001 enzymes for starch hydrolysis were carried out as simultaneous saccharification and fermentation. The grains and their corresponding dried distiller's grain with solubles (DDGS) were also analyzed for nutritional and value-added characteristics. A VHG traditional fermentation approach utilizing jet-cooking fermentation revealed that both dehulled Bold and Xena barley produced ethanol concentrations higher than that produced by wheat (12.3, 12.2, and 11.9%, respectively) but lower than that produced by corn (13.8%). VHG-modified Stargen-based fermentation of dehulled Bold barley demonstrated comparable performance (14.3% ethanol) relative to that of corn (14.5%) and wheat (13.3%). Several important components were found to survive fermentation and were concentrated in DDGS. The highest yield of phenolics was detected in the DDGS (modified Stargen 001, 20% solids) of Xena (14.6 mg of gallic acid/g) and Bold (15.0 mg of gallic acid/g) when the hull was not removed before fermentation. The highest concentration of sterols in DDGS from barley was found in Xena (3.9 mg/g) when the hull was included. The DDGS recovered from corn had the highest concentration of fatty acids (72.6 and 77.5 mg/g). The DDGS recovered from VHG jet-cooking fermentations of Fibar, dehulled Bold, and corn demonstrated similar levels of tocopherols and tocotrienols. Corn DDGS was highest in crude fat but was lowest in crude protein and in vitro energy digestibility. Wheat DDGS was highest in crude protein content, similar to previous studies. The barley DDGS was the highest in in vitro energy digestibility.
Poly-
N
-Acetylglucosamine Matrix Polysaccharide Impedes Fluid Convection and Transport of the Cationic Surfactant Cetylpyridinium Chloride through Bacterial Biofilms
Authors: Ganeshnarayan Krishnaraj , Shah Suhagi M. , Libera Matthew R. , Santostefano Anthony , Kaplan Jeffrey B.
Published: December 2008

Biofilms are composed of bacterial cells encased in a self-synthesized, extracellular polymeric matrix. Poly-β(1,6)-
N
-acetyl-
d
-glucosamine (PNAG) is a major biofilm matrix component in phylogenetically diverse bacteria. In this study we investigated the physical and chemical properties of the PNAG matrix in biofilms produced in vitro by the gram-negative porcine respiratory pathogen
Actinobacillus pleuropneumoniae
and the gram-positive device-associated pathogen
Staphylococcus epidermidis
. The effect of PNAG on bulk fluid flow was determined by measuring the rate of fluid convection through biofilms cultured in centrifugal filter devices. The rate of fluid convection was significantly higher in biofilms cultured in the presence of the PNAG-degrading enzyme dispersin B than in biofilms cultured without the enzyme, indicating that PNAG decreases bulk fluid flow. PNAG also blocked transport of the quaternary ammonium compound cetylpyridinium chloride (CPC) through the biofilms. Binding of CPC to biofilms further impeded fluid convection and blocked transport of the azo dye Allura red. Bioactive CPC was efficiently eluted from biofilms by treatment with 1 M sodium chloride. Taken together, these findings suggest that CPC reacts directly with the PNAG matrix and alters its physical and chemical properties. Our results indicate that PNAG plays an important role in controlling the physiological state of biofilms and may contribute to additional biofilm-associated processes such as biocide resistance.
Phleomycin Increases Transformation Efficiency and Promotes Single Integrations in
Schizophyllum commune
Authors: van Peer Arend F. , de Bekker Charissa , Vinck Arman , Wösten Han A. B. , Lugones Luis G.
Published: December 2008

Phleomycin is mutagenic by introducing double-strand breaks in DNA. The
ble
gene of
Streptoalloteychus hindustanus
, which confers resistance to this substance, is widely used as a selection marker for transformation.
Schizophyllum commune
grows on 25 μg of phleomycin ml
−1
after introduction of a resistance cassette based on the
ble
gene. However, we here report that growth of resistant colonies on this concentration of phleomycin resulted in aberrant colony morphologies. Apparently, phleomycin was mutagenic despite acquired resistance. Therefore, a new selection system was developed based on resistance to the antibiotic nourseothricin. However, the transformation efficiency was tenfold lower than that obtained with phleomycin as a selection agent. This low transformation efficiency could be rescued by addition of a nonselective concentration of phleomycin during protoplast regeneration. This was accompanied by a higher incidence of single-copy integrations and with an increase of expression of key genes involved in double-strand break repair. Taken together, we conclude that the effect of a nonselective concentration of phleomycin strongly resembles the effect of restriction enzyme-mediated integration (REMI) but, unlike REMI, it does not depend on the presence of a target restriction site.
Functional Analysis of Protein Kinase CK2 of the Human Malaria Parasite
Plasmodium falciparum
Authors: Holland Zoë , Prudent Renaud , Reiser Jean-Baptiste , Cochet Claude , Doerig Christian
Published: December 2008

Protein kinase CK2 (casein kinase 2) is a eukaryotic serine/threonine protein kinase with multiple substrates and roles in diverse cellular processes, including differentiation, proliferation, and translation. The mammalian holoenzyme consists of two catalytic alpha or alpha′ subunits and two regulatory beta subunits. We report the identification and characterization of a
Plasmodium falciparum
CK2α orthologue, PfCK2α, and two PfCK2β orthologues, PfCK2β1 and PfCK2β2. Recombinant PfCK2α possesses protein kinase activity, exhibits similar substrate and cosubstrate preferences to those of CK2α subunits from other organisms, and interacts with both of the PfCK2β subunits in vitro. Gene disruption experiments show that the presence of PfCK2α is crucial to asexual blood stage parasites and thereby validate the enzyme as a possible drug target. PfCK2α is amenable to inhibitor screening, and we report differential susceptibility between the human and
P. falciparum
CK2α enzymes to a small molecule inhibitor. Taken together, our data identify PfCK2α as a potential target for antimalarial chemotherapeutic intervention.
Trypanosoma brucei
UDP-Glucose:Glycoprotein Glucosyltransferase Has Unusual Substrate Specificity and Protects the Parasite from Stress
Authors: Izquierdo Luis , Atrih Abdel , Rodrigues Joao A. , Jones Deuan C. , Ferguson Michael A. J.
Published: December 2008

In this paper, we describe the range of N-linked glycan structures produced by wild-type and glucosidase II null mutant bloodstream form
Trypanosoma brucei
parasites and the creation and characterization of a bloodstream form
Trypanosoma brucei
UDP-glucose:glycoprotein glucosyltransferase null mutant. These analyses highlight peculiarities of the
Trypanosoma brucei
UDP-glucose:glycoprotein glucosyltransferase, including an unusually wide substrate specificity, ranging from Man
5
GlcNAc
2
to Man
9
GlcNAc
2
glycans, and an unusually high efficiency in vivo, quantitatively glucosylating the Asn263 N-glycan of variant surface glycoprotein (VSG) 221 and 75% of all non-VSG N glycosylation sites. We also show that although
Trypanosoma brucei
UDP-glucose:glycoprotein glucosyltransferase is not essential for parasite growth at 37°C, it is essential for parasite growth and survival at 40°C. The null mutant was also shown to be hypersensitive to the effects of the N glycosylation inhibitor tunicamycin. Further analysis of bloodstream form
Trypanosoma brucei
under normal conditions and stress conditions suggests that it does not have a classical unfolded protein response triggered by sensing unfolded proteins in the endoplasmic reticulum. Rather, judging by its uniform Grp78/BiP levels, it appears to have an unregulated and constitutively active endoplasmic reticulum protein folding system. We suggest that the latter may be particularly appropriate for this organism, which has an extremely high flux of glycoproteins through its secretory pathway.
Porphyromonas gingivalisRgpA-Kgp Proteinase-Adhesin Complexes Penetrate Gingival Tissue and Induce Proinflammatory Cytokines or Apoptosis in a Concentration-Dependent Manner
Authors: O'Brien-Simpson Neil M. , Pathirana Rishi D. , Walker Glenn D. , Reynolds Eric C.
Published: December 2008

The RgpA-Kgp proteinase-adhesin complexes ofPorphyromonas gingivaliswere observed, using immunostaining, in human gingival tissue associated with periodontitis but not in healthy tissue. The staining pattern suggested a concentration gradient from the subgingival plaque into the subjacent gingival connective tissue. Intense immunostaining was observed in areas displaying gross disturbance of tissue architecture.P. gingivaliscells and the RgpA-Kgp complexes at low concentrations were shown to stimulate secretory intercellular adhesion molecule 1, interleukin-8 (IL-8), IL-6, and macrophage chemoattractant protein secretion from cultured human epithelial (KB) and fibroblast (MRC-5) cells. However, at high concentrations a reduction in the level of these mediators was observed. In contrast, macrophage inflammatory protein 1α and IL-1α were stimulated only at highP. gingivaliscell concentrations.P. gingivaliscells and the RgpA-Kgp complexes were shown to induce apoptosis in KB and MRC-5 cells in a time- and dose-dependent manner. These data suggest that the RgpA-Kgp complexes penetrate the gingival connective tissue; at low concentrations distal from the plaque the complexes stimulate the secretion of proinflammatory mediators, while at high concentrations proximal to the plaque they induce apoptosis and attenuate the secretion of proinflammatory mediators.
The CiaR Response Regulator in Group BStreptococcusPromotes Intracellular Survival and Resistance to Innate Immune Defenses
Authors: Quach Darin , van Sorge Nina M. , Kristian Sascha A. , Bryan Joshua D. , Shelver Daniel W. , Doran Kelly S.
Published: December 2008

Group BStreptococcus(GBS) is major cause of invasive disease in newborn infants and the leading cause of neonatal meningitis. To gain access to the central nervous system (CNS), GBS must not only subvert host defenses in the bloodstream but also invade and survive within brain microvascular endothelial cells (BMEC), the principal cell layer composing the blood-brain barrier (BBB). While several GBS determinants that contribute to the invasion of BMEC have been identified, little is known about the GBS factors that are required for intracellular survival and ultimate disease progression. In this study we sought to identify these factors by screening a random GBS mutant library in an in vitro survival assay. One mutant was identified which contained a disruption in a two-component regulatory system homologous to CiaR/CiaH, which is present in other streptococcal pathogens. Deletion of the putative response regulator,ciaR, in GBS resulted in a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC, which was linked to increased susceptibility to killing by antimicrobial peptides, lysozyme, and reactive oxygen species. Furthermore, competition experiments with mice showed that wild-type GBS had a significant survival advantage over the GBS ΔciaRmutant in the bloodstream and brain. Microarray analysis comparing gene expression between wild-type and ΔciaRmutant GBS bacteria revealed several CiaR-regulated genes that may contribute to stress tolerance and the subversion of host defenses by GBS. Our results identify the GBS CiaR response regulator as a crucial factor in GBS intracellular survival and invasive disease pathogenesis.
Genetic Evidence for the Importance of Protein Acetylation and Protein Deacetylation in the Halophilic Archaeon
Haloferax volcanii
Authors: Altman-Price Neta , Mevarech Moshe
Published: December 2008

Protein acetylation and deacetylation reactions are involved in many regulatory processes in eukaryotes. Recently, it was found that similar processes occur in bacteria and archaea. Sequence analysis of the genome of the haloarchaeon
Haloferax volcanii
led to the identification of three putative protein acetyltransferases belonging to the Gcn5 family, Pat1, Pat2, and Elp3, and two deacetylases, Sir2 and HdaI. Intriguingly, the gene that encodes HdaI shares an operon with an archaeal histone homolog. We performed gene knockouts to determine whether the genes encoding these putative acetyltransferases and deacetylases are essential. A
sir2
deletion mutant was able to grow normally, whereas an
hdaI
deletion mutant was nonviable. The latter is consistent with the finding that trichostatin A, a specific inhibitor of HdaI, inhibits cell growth in a concentration-dependent manner. We also showed that each of the acetyltransferases by itself is dispensable for growth but that deletion of both
pat2
and
elp3
could not be achieved. The corresponding genes are therefore “synthetic lethals,” and the protein acetyltransferases probably have a common and essential substrate.
Ferredoxin-NADP
+
Reductase from
Pseudomonas putida
Functions as a Ferric Reductase
Authors: Yeom Jinki , Jeon Che Ok , Madsen Eugene L. , Park Woojun
Published: December 2008

Pseudomonas putida
harbors two ferredoxin-NADP
+
reductases (Fprs) on its chromosome, and their functions remain largely unknown. Ferric reductase is structurally contained within the Fpr superfamily. Interestingly, ferric reductase is not annotated on the chromosome of
P. putida
. In an effort to elucidate the function of the Fpr as a ferric reductase, we used a variety of biochemical and physiological methods using the wild-type and mutant strains. In both the ferric reductase and flavin reductase assays, FprA and FprB preferentially used NADPH and NADH as electron donors, respectively. Two Fprs prefer a native ferric chelator to a synthetic ferric chelator and utilize free flavin mononucleotide (FMN) as an electron carrier. FprB has a higher
k
cat
/

K
m

value for reducing the ferric complex with free FMN. The growth rate of the
fprB
mutant was reduced more profoundly than that of the
fprA
mutant, the growth rate of which is also lower than the wild type in ferric iron-containing minimal media. Flavin reductase activity was diminished completely when the cell extracts of the
fprB
mutant plus NADH were utilized, but not the
fprA
mutant with NADPH. This indicates that other NADPH-dependent flavin reductases may exist. Interestingly, the structure of the NAD(P) region of FprB, but not of FprA, resembled the ferric reductase (Fre) of
Escherichia coli
in the homology modeling. This study demonstrates, for the first time, the functions of Fprs in
P. putida
as flavin and ferric reductases. Furthermore, our results indicated that FprB may perform a crucial role as a NADH-dependent ferric/flavin reductase under iron stress conditions.
Growth Phase- and Cell Division-Dependent Activation and Inactivation of the σ
32
Regulon in
Escherichia coli
Authors: Wagner Maria Anna , Zahrl Doris , Rieser Gernot , Koraimann Günther
Published: December 2008

Alternative sigma factors allow bacteria to reprogram global transcription rapidly and to adapt to changes in the environment. Here we report on growth- and cell division-dependent σ
32
regulon activity in
Escherichia coli
in batch culture. By analyzing σ
32
expression in growing cells, an increase in σ
32
protein levels is observed during the first round of cell division after exit from stationary phase. Increased σ
32
protein levels result from transcriptional activation of the
rpoH
gene. After the first round of bulk cell division,
rpoH
transcript levels and σ
32
protein levels decrease again. The late-logarithmic phase and the transition to stationary phase are accompanied by a second increase in σ
32
levels and enhanced stability of σ
32
protein but not by enhanced transcription of
rpoH
. Throughout growth, σ
32
target genes show expression patterns consistent with oscillating σ
32
protein levels. However, during the transition to early-stationary phase, despite high σ
32
protein levels, the transcription of σ
32
target genes is downregulated, suggesting functional inactivation of σ
32
. It is deduced from these data that there may be a link between σ
32
regulon activity and cell division events. Further support for this hypothesis is provided by the observation that in cells in which FtsZ is depleted, σ
32
regulon activation is suppressed.
Regulation of Cyclic Lipopeptide Biosynthesis inPseudomonas fluorescensby the ClpP Protease
Authors: de Bruijn I. , Raaijmakers J. M.
Published: December 2008

Cyclic lipopeptides produced byPseudomonasspecies exhibit potent surfactant and broad-spectrum antibiotic properties. Their biosynthesis is governed by large multimodular nonribosomal peptide synthetases, but little is known about the genetic regulatory network. This study provides, for the first time, evidence that the serine protease ClpP regulates the biosynthesis of massetolides, cyclic lipopeptides involved in swarming motility, biofilm formation, and antimicrobial activity ofPseudomonas fluorescensSS101. The results show that ClpP affects the expression ofluxR(mA), the transcriptional regulator of the massetolide biosynthesis genesmassABC, thereby regulating biofilm formation and swarming motility ofP. fluorescensSS101. Transcription ofluxR(mA) was significantly repressed in theclpPmutant, and introduction ofluxR(mA) restored, in part, massetolide biosynthesis and swarming motility of theclpPmutant. Site-directed mutagenesis and expression analyses indicated that the chaperone subunit ClpX and the Lon protease are not involved in regulation of massetolide biosynthesis and are transcribed independently ofclpP. Addition of Casamino Acids enhanced the transcription ofluxR(mA) andmassABCin theclpPmutant, leading to a partial rescue of massetolide production and swarming motility. The results further suggested that, at the transcriptional level, ClpP-mediated regulation of massetolide biosynthesis operates independently of regulation by the GacA/GacS two-component system. The role of amino acid metabolism and the putative mechanisms underlying ClpP-mediated regulation of cyclic lipopeptide biosynthesis, swarming motility, and growth inP. fluorescensare discussed.
PP-WAVES ON SUPERBRANE BACKGROUNDS
Authors: CAVAGLIÀ MARCO , HARMS BENJAMIN
Published: December 2008

In this paper we discuss a method of generating solutions of the Einstein equations on supersymmetric and non-supersymmetric backgrounds. The method involves the embedding of a supersymmetric spacetime into another, curved spacetime. We present three examples with constituent spacetimes which support "charges", one of which was known previously and the other two of which are new. All of the examples have PP-waves as one of the embedding constituents.
PHASE SPACE POLARIZATION AND THE TOPOLOGICAL STRING: A CASE STUDY
Authors: KASHANI-POOR AMIR-KIAN
Published: December 2008

We review and elaborate on our discussion in hep-th/0606112 on the interplay between the target space and the worldsheet description of the open topological string partition function, for the example of the conifold. We discuss the appropriate phase space and canonical form for the system. We find a map between choices of polarization and the worldsheet description, based on which we study the behavior of the partition function under canonical transformations.
COMPUTING ALTERNATING OFFERS AND WATER PRICES IN BILATERAL RIVER BASIN MANAGEMENT
Authors: HOUBA HAROLD
Published: December 2008

This contribution addresses the fundamental critique in Dinar et al. [1992, Theory and Decision32] on the use of game theory in river basin management: People are reluctant to monetary transfers unrelated to water prices and game theoretic solutions impose a computational burden. For the bilateral alternating-offers model, a single optimization program significantly reduces the computational burden. Furthermore, water prices and property rights result from exploiting the Second Welfare Theorem. Both issues are discussed and applied to a bilateral version of the theoretical river basin model in Ambec and Sprumont [2002, Journal of Economic Theory107]. Directions for future research are provided.
d-WISE GENERATION OF SOME INFINITE GROUPS
Authors: LUCCHINI ANDREA , MARÓTI ATTILA , SEMMEN DARREN
Published: December 2008

What is the largest possible size of a subset of SL(n,ℤ) from which every pair of elements will be a generating set? We prove a general result on generation probabilities in profinite groups that suggests the cardinality of a maximal such subset equals that of the analogous subset of SL(n, ℤ/2ℤ).
ON FINITE GALOIS STABLE ARITHMETIC GROUPS AND THEIR APPLICATIONS
Authors: KHREBTOVA EKATERINA S. , MALININ DMITRY
Published: December 2008

We prove the existence and finiteness theorems for integral representations stable under Galois operation. An explicit construction of the realization fields for representations of finite groups stable under the natural operation of the Galois group is given. We also compare the representations over fields and the rings of integers, and give a quantitative result on the rarity of integral Galois stable representations. There is a series of related conjectures and applications to arithmetic algebraic geometry, finite flat group schemes, positive definite quadratic lattices and Galois cohomology.
THE DEVELOPMENT OF A COMPUTER-ASSISTED TOOL FOR THE ASSESSMENT OF NEUROPSYCHOLOGICAL DRAWING TASKS
Authors: GLENAT STEPHANIE , HEUTTE LAURENT , PAQUET THIERRY , GUEST RICHARD , FAIRHURST MICHAEL , LINNELL TRISTAN
Published: December 2008

In a previous paper, we highlighted the design requirements of a computer-based system for the automated assessment of neuropsychological drawing tasks. In this paper, we shall examine the implementation of an analysis system specifically with reference to the software engineering principles utilized and the modular framework within with a flexible implementation can be realized. We shall highlight some of the implemented modules and, using two actual test batteries as examples, demonstrate the flow of information between each module. We shall also show the additional reporting and analysis features implemented for clinician support and describe how the framework can be utilized for more generic applications of handwriting/drawing analysis.
DETERMINING AGGREGATE CRITERIA WEIGHTS FROM CRITERIA RANKINGS BY A GROUP OF DECISION MAKERS
Authors: ALFARES HESHAM K. , DUFFUAA SALIH O.
Published: December 2008

In this paper, we present an empirical methodology to determine aggregate numerical criteria weights from group ordinal ranks of multiple decision criteria. Assuming that such ordinal ranks are obtained from several decision makers, aggregation procedures are proposed to combine individual rank inputs into group criteria weights. In this process, we use previous empirical results for an individual decision maker, in which a simple function provides the weight for each criterion as a function of its rank and the total number of criteria. Using a set of experiments, weight aggregation procedures are proposed and empirically compared for two cases: (i) when all the decision makers rank the same set of criteria, and (ii) when they rank different subsets of criteria. The proposed methodology can be used to determine relative weights for any set of criteria, given only criteria ranks provided by several decision makers.
MULTIPARTY QUANTUM SECRET SHARING OF SECURE DIRECT COMMUNICATION WITH HIGH-DIMENSIONAL QUANTUM SUPERDENSE CODING
Authors: WANG XIN , LIU YI-MIN , HAN LIAN-FANG , ZHANG ZHAN-JUN
Published: December 2008

The first protocol of multiparty quantum secret sharing of secure direct communication [Phys. Lett. A342 (2005) 60] is generalized to the high-dimensional case via quantum superdense coding. The generalized protocol has the advantages of higher capacity and better security.
MIXING OF QUANTUM WALKS ON GENERALIZED HYPERCUBES
Authors: BEST ANA , KLIEGL MARKUS , MEAD-GLUCHACKI SHAWN , TAMON CHRISTINO
Published: December 2008

We study continuous-time quantum walks on graphs which generalize the hypercube. The only known family of graphs whose quantum walk instantaneously mixes to uniform is the Hamming graphs with small arities. We show that quantum uniform mixing on the hypercube is robust under the addition of perfect matchings but not much else. Our specific results include:

• The graph obtained by augmenting the hypercube with an additive matching x ↦ x ⊕ η is instantaneous uniform mixing whenever |η| is even, but with a slower mixing time. This strictly includes the result of Moore and Russell1on the hypercube.

• The class of Hamming graphs H(n,q) is not uniform mixing if and only if q ≥ 5. This is a tight characterization of quantum uniform mixing on Hamming graphs; previously, only the status of H(n,q) with q < 5 was known.

• The bunkbed graph [Formula: see text] whose adjacency matrix is I ⊗ Qn+ X ⊗ Af, where Afis a [Formula: see text]-circulant matrix defined by a Boolean function f, is not uniform mixing if the Fourier transform of f has support of size smaller than 2n-1. This explains why the hypercube is uniform mixing and why the join of two hypercubes is not.

Our work exploits the rich spectral structure of the generalized hypercubes and relies heavily on Fourier analysis of group-circulants.
MINIMAL CLASSICAL COMMUNICATION COST AND MEASUREMENT COMPLEXITY IN SPLITTING TWO-QUBIT QUANTUM INFORMATION VIA ASYMMETRIC W STATES
Authors: ZUO XUE-QIN , LIU YI-MIN , ZHANG WEN , YIN XIAO-FENG , ZHANG ZHAN-JUN
Published: December 2008

We propose a scheme for splitting a two-qubit quantum information by using two asymmetric W states as quantum channel. In this scheme the split state is assumed to be completely known by the sender. Because of this, during the splitting process, the sender only needs to perform a two-qubit projective measurement. Once the sender announces the measurement result in terms of the prior agreement, then using this message the two receivers can recover the quantum information via their mutual assistance. We calculate the success probability and classical communication cost of the scheme. In general, the splitting success probability (SSP) is 1/4 and the average classical communication cost is 0.25 bit. However, we find that for some states the SSP can reach 0.5 or even unity after consuming a little additional classical resource.
QUANTUM ERROR-CORRECTING CODES FROM QUASI-CYCLIC CODES
Authors: QIAN JIANFA , MA WENPING , WANG XINMEI
Published: December 2008

Quasi-cyclic codes form a generalization of cyclic codes, and contain a large number of record breaking codes. In this paper, we provide a method for constructing self-orthogonal quasi-cyclic codes, and obtain a large number of new quantum quasi-cyclic codes by CSS construction.
MULTILINEAR MAPPING AND STRUCTURE OF MULTIPARTITE STATES
Authors: HEYDARI HOSHANG
Published: December 2008

We investigate the relation between multilinear mappings and multipartite states. We show that the isomorphism between multilinear mapping and tensor product completely characterizes decomposable multipartite states in a mathematically well-defined manner.
DB&IR integration
Authors: Amer-Yahia Sihem , Hiemstra Djoerd , Roelleke Thomas , Srivastava Divesh , Weikum Gerhard
Published: December 2008

This paper is based on a five-day workshop on "Ranked XML Querying" that took place in Schloss Dagstuhl in Germany in March 2008 and was attended by 27 people from three different research communities: database systems (DB), information retrieval (IR), and Web. The seminar title was interpreted in an IR-style "andish" sense (it covered also subsets of {Ranking, XML, Querying}, with larger sets being favored) rather than the DB-style strictly conjunctive manner. So in essence, the seminar really addressed the integration of DB and IR technologies with Web 2.0 being an important target area.
Injecting programming language concepts throughout the curriculum
Authors: Bailey Mark W.
Published: December 2008

As research in programming language design,implementation,and application advances,we must regu- larly revisit the undergraduate curriculum to ensure course content advances similarly.However,no matter how diligent our efforts,the undergraduate curriculum will continue to undergo pressure from all fields of the discipline to include courses covering those fields.Though we could advocate for core placement of programming language courses,it is likely,even inevitable,that a growing number of colleges and universi- ties will choose not to mandate programming language courses for their degree programs.Thus,we must develop an inclusive strategy that encourages the teaching of programming language topics even in colleges and universities that choose not to devote an entire course to the study of them.I have proposed one such strategy that supports the injection of programming language concepts into other courses of interest to both students and faculty.
Why teach programming languages in this day and age and how to go about it
Authors: Felleisen Matthias
Published: December 2008

The question is not whether a computing curriculum should include a rigorous course on programming languages, but which topics make up the minimum that we wish every student to understand, and how we should teach these topics.
MeanField analysis for the evaluation of gossip protocols
Authors: Bakhshi Rena , Cloth Lucia , Fokkink Wan , Haverkort Boudewijn R.
Published: December 2008

Gossip protocols are designed to operate in very large, decentralised networks. A node in such a network bases its decision to interact (gossip) with another node on its partial view of the global system. Because of the size of these networks, analysis of gossip protocols is mostly done using simulation, which tend to be expensive in computation time and memory consumption.

We introduce mean-field analysis as an analytical method to evaluate gossip protocols. Nodes in the network are represented by small identical stochastic models. Joining all nodes would result in an enormous stochastic process. If the number of nodes goes to infinity, however, mean-field analysis allows us to replace this intractably large stochastic process by a small deterministic process. This process approximates the behaviour of very large gossip networks, and can be evaluated using simple matrix-vector multiplications.