bluuebunny/crossref_metadata_2025 huggingface dataset:
A consumer‐oriented technique for planned residential developments
Authors: Majamaa Wisa , Kuronen Matti , Heywood Chris , Kostiainen Juha
Published: August 2008

Purpose

The purpose of this paper is to examine the identification and engagement of future inhabitants in planning processes for residential developments using a new “4Ps” participation method, where the 4Ps denote public, private and people are in partnership. This form of participation gives new information, related to consumers' residential choice, unlike those environments produced by using other participation methods.

Design/methodology/approach

The empirical study is based on innovation theory where end‐users are primary stakeholders in the innovation process, and even innovators themselves. A case study of a new participation method based on a two‐phase internet questionnaire is used to research practical solutions in integrating end‐users into urban planning process.

Findings

This paper demonstrates that the widely used theory of communicative action in planning and its aim of increasing citizens' activity in planning and development processes can be developed to the stage that it also includes future inhabitants as stakeholders. Thus urban planning processes become innovative and customer‐oriented through their openness, end‐user orientation and interpretative nature.

Originality/value

The case study findings indicate that the new participation method described here gives flexibility and benefits to all stakeholders and is a method to create consumer‐desirable neighbourhoods. Engaging future inhabitants in planning processes opens previously unseen potential for including consumerist possibilities for cities and developers. This paper illustrates that this new 4Ps participation method makes comprehensive participatory planning and development possible through giving an opportunity to include consumers' opinions and needs into an alternative to traditional communicative planning.
Choice criteria for Islamic home financing
Authors: Amin Hanudin
Published: August 2008

Purpose

The purpose of this paper is to investigate the choice criteria for Islamic home financing in Malaysian Islamic banks. Most importantly, this study considers establishing a specific rank of choice criteria for Islamic home financing. Moreover, these choice criteria will also be ranked according to the selected demographic elements such as gender, marital status and age range.

Design/methodology/approach

This study uses a quantitative study similar to what was employed by previous researchers. The study presents primary data collected by self‐administered questionnaires involving a sample of 150 Malaysian bank customers in Labuan, Malaysia. Of these, 141 questionnaires were returned with a response rate equivalent to 94 per cent. The Islamic home financing choice criteria as perceived by the Malaysian bank customers are analysed using frequencies, independent samples t‐test and ANOVA.

Findings

The results suggest that “Shariah principle”, “lower monthly payment”, “transparency practice”, “interest‐free practice” and “100 per cent financing” are the first five decision criteria considered as being very important. The least preferred criteria, among others, are “recommendation”, “longer financing period”, “product range” and “branch location”. Results also suggested that a small number of significant differences are apparent in the importance of choice criteria with respect to gender, marital status and age range.

Research limitations/implications

The study contains three limitations. The first limitation was based on the sample area for the study which is confined to Labuan, Malaysia. Second, this study restricted the use of factor analysis since the data did not allow for aggregation. Third, this study was also unable to perform ANOVA for religion differences as the sample consisted largely of Muslims.

Practical implications

The results are primarily beneficial to academics and practitioners in Malaysia by offering an insight into choice criteria for Islamic home financing. This study provides new results about different kinds of customer types and their preferences with regards to Islamic home financing selection. As such, Islamic bank managers can learn and plan to offer attractive schemes for the Islamic home financing market that meet Malaysian bank customers' needs. For the researcher, this study contributes to existing body of knowledge by providing an investigation of choice criteria in the Islamic home financing. Indeed, this study is considered an “eye‐opener” for Islamic home financing choice criteria which has limited previous studies. Originality/value –This study introduces the choice criteria for Islamic financing among Malaysian bank customers. The study offers an insight into Islamic home financing choice criteria in Malaysia which has limited previously been investigated.
The Islamic inter bank money market and a dual banking system: the Malaysian experience
Authors: Ismath Bacha Obiyathulla
Published: August 2008

Purpose

This paper seeks to examine the operation of an Islamic inter‐bank money market (IIMM), within a dual banking system.

Design/methodology/approach

The paper describes Malaysia's Islamic IIMM. It then examines some of the key risks associated with money market functions. An empirical examination of the extent to which yields in the IIMM are correlated with conventional money market yields is undertaken. The implication of this on interest‐rate exposure for the Islamic financial sector is discussed. Finally, the paper looks at some of the challenges and offers conclusions.

Findings

The paper argues that even though an Islamic money market operates in an interest‐free environment and trades Shariah‐compliant instruments, many of the risks associated with conventional money markets, including interest‐rate risks are relevant. The empirical evidence, based on Malaysian data, points to Islamic money market profit rates/yields that are highly correlated and move in tandem with conventional money market rates. Given the dynamics of fund flows and cross‐linkages, an IIMM operating within a dual banking system cannot sterilize itself from interest‐rate risks. In fact, the paper argues that such an IIMM may actually enhance interest‐rate risk transmission to the Islamic banking sector, by providing additional channels of transmission. Ironical as it may be, the operations of an IIMM in a dual banking system may serve to bring the Islamic banking sector into closer orbit with the conventional sector.

Originality/value

The paper offers insights into the IIMM, focusing on Malaysia.
Systematic review: hepatic fibrosis – regression with therapy
Authors: ZOIS C. D. , BALTAYIANNIS G. H. , KARAYIANNIS P. , TSIANOS E. V.
Published: August 2008

Background  Hepatic fibrosis occurs in response to chronic liver injury, regardless of the cause. An impressive amount of knowledge concerning the pathogenesis and treatment of liver fibrosis has emerged over the past few years. The hallmark of this event is the activation of the hepatic stellate cell. The latter event causes accumulation of extracellular matrix and formation of scar, leading to deterioration in hepatic function.

Aim  To assess chronic liver injury, many invasive and non‐invasive methods have been suggested.

Methods  Although transient elastography, image analysis of fractal geometry and fibrotest with actitest have been used in clinical practice, liver biopsy remains the recommended choice, especially when histological staging of fibrosis or response to treatment is needed.

Conclusions  The recent advances in anti‐viral therapy have resulted in many reports on fibrosis and even on cirrhosis regression, especially early and in young people. A number of new agents have been suggested for the treatment of fibrosis, with promising results in animals; however, their efficacy in humans remains to be elucidated. The investigation of heterogeneity and plasticity of hepatic stellate cells is a topic of scientific interest and may result in improvements in patient management.
Effect of chronic exposure to morphine on the rat blood–brain barrier: focus on the P‐glycoprotein
Authors: Yousif Salah , Saubaméa Bruno , Cisternino Salvatore , Marie‐Claire Cynthia , Dauchy Sandrine , Scherrmann Jean‐Michel , Declèves Xavier
Published: August 2008

Morphine may affect the properties of the blood–brain barrier (BBB) by modifying the expression of certain BBB markers. We have determined the effect of chronic morphine treatment on the expression and function of some BBB markers in the rat. The mRNAs of 19 selected genes encoding caveolins, endothelial transporters, receptors and tight junctions proteins in the total RNA of isolated cortex microvessels were assayed by quantitative RT‐PCR (qRT‐PCR). The expression of genesMdr1a, Mrp1, Bcrp, Glut‐1andOccludin, was slightly increased, while that ofFlk‐1was decreased in microvessels from morphine‐treated rats. The expression of theMrd1aandMdr1bgenes encoding the P‐glycoprotein (P‐gp) also increased in the whole hippocampus and cortex of morphine‐treated rats. TheMdr1agene induction (1.38‐fold) observed by qRT‐PCR was also confirmed usingin situhybridization technique (1.40‐fold). Immunoblotting revealed an increase in P‐gp expression in the hippocampus (1.8‐fold) and cortex (1.36‐fold) of morphine‐treated rats, but no effect in isolated microvessels. In contrast, morphine treatment increased by 1.48‐fold the expression of P‐gp in a large vessel‐enriched fraction. The integrity of the BBB, measured byin situbrain perfusion of [14C]‐sucrose, and the activity of P‐gp at the BBB, measured with the P‐gp substrate [3H]‐colchicine, were not modified by morphine. Immunohistofluorescence experiments revealed that P‐gp expression is restricted to large vessels and microvessels in control rats and that morphine treatment did not induce the expression of P‐gp in the brain parenchyma (astrocytes or neurons). Taken together, our results showed that chronic morphine treatment does not significantly alter BBB integrity or P‐gp activity. The impact of morphine‐mediated P‐gp induction observed in large vessels remains to be determined in terms of brain disposition of drugs that are P‐gp substrates.
Pressure-Scaling of Pressure-Swirl Atomizer Cone Angles
Authors: Guildenbecher D. R. , Rachedi R. R. , Sojka P. E.
Published: August 2008

An experimental investigation was conducted to study the effects of increased ambient pressure (up to 6.89MPa) and increased nozzle pressure drop (up to 2.8MPa) on the cone angles for sprays produced by pressure-swirl atomizers having varying amounts of initial swirl. This study extends the classical results of DeCorso and Kemeny, (1957, “Effect of Ambient and Fuel Pressure on Nozzle Spray Angle,” ASME Transactions, 79(3), pp. 607–615). Shadow photography was used to measure cone angles at x∕D0=10, 20, 40, and 60. Our lower pressure results for atomizer swirl numbers of 0.50 and 0.25 are consistent with those of DeCorso and Kemeny, who observed a decrease in cone angle with an increase in nozzle pressure drop, ΔP, and ambient density, ρair, until a minimum cone angle was reached when ΔPρair1.6∼100MPa(kg∕m3)1.6 (equivalent to 200psi(lbm∕ft3)1.6). Results for atomizers having higher initial swirl do not match the DeCorso and Kemeny results as well, suggesting that their correlation be used with caution. Another key finding is that an increase in ΔPρair1.6 to a value of 600MPa(kg∕m3)1.6 leads to continued decrease in cone angle, but that a subsequent increase to 2000MPa(kg∕m3)1.6 has little effect on cone angle. Finally, there was little effect of nozzle pressure drop on cone angle, in contrast to findings of previous workers. These effects are hypothesized to be due to gas entrainment.
A Case Study for a Turbogenerator Accident Using Multiscale Association
Authors: Yu Da-Ren , Wang Wei , Zhang Zhi-Qiang , Hu Qing-Hua , Zhao Xiao-Min
Published: August 2008

This paper presents a novel method of multiscale association for analyzing a turbogenerator accident having strange behaviors and serious consequence. Wave index (WI) and credibility of sensor fault are proposed based on multiscale analysis of the recorded data, and then the associational degree of WI is used to detect sensor fault. In addition, mechanism models are built to verify that detection. Furthermore, maximum likelihood method and neural network are applied to estimate the confidence interval of the fault sensor and the true signal. The estimation has been used to clearly explain the cause of this accident.
Biaxial Thermomechanical-Fatigue Life Property of a Directionally Solidified Ni-Base Superalloy
Authors: Ogata Takashi
Published: August 2008

High-temperature components in thermal power plants are subjected to creep-fatigue loading where creep cavities initiate and grow on grain boundaries. Development of life assessment methods of high-temperature components in gas turbine for maintenance and operating cost reduction is strongly demanded by Japanese utilities. Especially, first row blades are subjected to complicated thermomechanical-fatigue (TMF) loading during start, steady state, stop cycles. Therefore it is important to clarify the TMF life property of blade materials to develop a life assessment procedure. In this study, tension-torsion biaxial TMF tests have been performed between 450°C and 870°C on a Ni-base directional solidified superalloy. Strain ratio ϕ was defined as shear strain range, Δγ, to normal strain range, Δε, and ϕ varied from 0 to infinity. The “Blade wave form,” which simulated temperature and strain condition of the blade surface, was employed. The biaxial TMF tests were also carried out on coated specimens with CoCrAlY. Fatigue life under the biaxial TMF loading showed strain ratio dependency giving shorter life with increasing ϕ. Considering biaxial stress effect on the failure life, an equivalent shear strain range was derived based on the Γ-plane theory, and the biaxial TMF life was well correlated with the equivalent shear strain range. The biaxial TMF life was reduced by introducing strain hold duration at the maximum temperature. The maximum stress increased by introducing the hold time due to increasing mean stress level in the Blade wave form. It was concluded that creep damage gradually accumulated during cycles resulting in reduction in the TMF life. The nonlinear creep-fatigue damage accumulation model was applied to predict failure life of the hold time tests. As a result, the failure lives were predicted within a factor of 1.5 on the observed life. It was found that the fatigue life of CoCrAlY coated material reduced 1∕2 to 1∕3 from that of the substrate. From observation of the longitudinal section of the coated specimens, many cracks started from the coating surface and penetrated into the substrate. It was concluded that the CoCrAlY coating reduced the biaxial TMF life due to acceleration of crack initiation period in the substrate.
Improving the Performance of a Bent Ejector With Inlet Swirl
Authors: Maqsood Asim , Birk A. M.
Published: August 2008

Ejectors are commonly employed in gas turbine exhaust systems for reasons such as space ventilation and IR suppression. Ejectors may incorporate bends in the geometry for various reasons. Studies have shown that the bend has a deteriorating effect on the performance of an ejector. This work was aimed to investigate the effect of exhaust gas swirl on improving the performance of a bent ejector. Four short oblong ejectors with different degrees of bend in the mixing tube and four swirl conditions were tested in this study. The primary nozzle, in all cases, was composed of a circular to oblong transition. Testing was performed at ambient and hot primary flow with 0deg, 10deg, 20deg, and 30deg swirl angles. It was observed that the swirl had a strong affect on the performance of a bent ejector. Improvement of up to 55%, 96%, and 180% was obtained in the pumping ratio, pressure rise, and total efficiency, respectively, with a 20deg swirl in the exhaust gas.
Sources of Clostridia in Raw Milk on Farms
Authors: Julien Marie-Claude , Dion Patrice , Lafrenière Carole , Antoun Hani , Drouin Pascal
Published: August 2008

A PCR-denaturing gradient gel electrophoresis (DGGE) method was used to examine on-farm sources of
Clostridium
cluster I strains in four dairy farms over 2 years. Conventional microbiological analysis was used in parallel to monitor size of clostridial populations present in various components of the milk production chain (soil, forage, grass silage, maize silage, dry hay, and raw milk). PCR amplification with
Clostridium
cluster I-specific 16S rRNA gene primers followed by DGGE separation yielded a total of 47 operational taxonomic units (OTUs), which varied greatly with respect to frequency of occurrence. Some OTUs were found only in forage, and forage profiles differed according to farm location (southern or northern Québec). More clostridial contamination was found in maize silage than in grass silage. Milk represented a potential environment for certain OTUs. No OTU was milk specific, indicating that OTUs originated from other environments. Most (83%) of the OTUs detected in raw milk were also found in grass or maize silage. Milk DGGE profiles differed according to farm and sampling year and fit into two distinct categories. One milk profile category was characterized by the presence of a few dominant OTUs, the presence of which appeared to be more related to farm management than to feed contamination. OTUs were more varied in the second profile category. The identities of certain OTUs frequently found in milk were resolved by cloning and sequencing.
Clostridium disporicum
was identified as an important member of clostridial populations transmitted to milk.
Clostridium tyrobutyricum
was consistently found in milk and was widespread in the other farm environments examined.
Specific DNA Binding of a Potential Transcriptional Regulator, Inosine 5′-Monophosphate Dehydrogenase-Related Protein VII, to the Promoter Region of a Methyl Coenzyme M Reductase I-Encoding Operon Retrieved from
Methanothermobacter thermautotrophicus
Strain ΔH
Authors: Shinzato Naoya , Enoki Miho , Sato Hiroaki , Nakamura Kohei , Matsui Toru , Kamagata Yoichi
Published: August 2008

Two methyl coenzyme M reductases (MCRs) encoded by the
mcr
and
mrt
operons of the hydrogenotrophic methanogen
Methanothermobacter thermautotrophicus
ΔH are expressed in response to H
2
availability. In the present study,
cis
elements and
trans
-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from
mrt
-expressing cultures restricted them to 46- and 41-bp-long
mcr
and
mrt
upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine β-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the
mcr
operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the
mcr
operon in this methanogen.
Multilocus Sequence Typing and Phylogenetic Analyses of
Pseudomonas aeruginosa
Isolates from the Ocean
Authors: Khan Nurul Huda , Ahsan Mahbuba , Yoshizawa Susumu , Hosoya Shoichi , Yokota Akira , Kogure Kazuhiro
Published: August 2008

Recent isolation of
Pseudomonas aeruginosa
strains from the open ocean and subsequent pulsed-field gel electrophoresis analyses indicate that these strains have a unique genotype (N. H. Khan, Y. Ishii, N. Kimata-Kino, H. Esaki, T. Nishino, M. Nishimura, and K. Kogure, Microb. Ecol. 53:173-186, 2007). We hypothesized that ocean
P. aeruginosa
strains have a unique phylogenetic position relative to other strains. The objective of this study was to clarify the intraspecies phylogenetic relationship between marine strains and other strains from various geographical locations. Considering the advantages of using databases, multilocus sequence typing (MLST) was chosen for the typing and discrimination of ocean
P. aeruginosa
strains. Seven housekeeping genes (
acsA
,
aroE
,
guaA
,
mutL
,
nuoD
,
ppsA
, and
trpE
) were analyzed, and the results were compared with data on the MLST website. These genes were also used for phylogenetic analysis of
P. aeruginosa
. Rooted and unrooted phylogenetic trees were generated for each gene locus and the concatenated gene fragments. MLST data showed that all the ocean strains were new. Trees constructed for individual and concatenated genes revealed that ocean
P. aeruginosa
strains have clusters distinct from those of other
P. aeruginosa
strains. These clusters roughly reflected the geographical locations of the isolates. These data support our previous findings that
P. aeruginosa
strains are present in the ocean. It can be concluded that the ocean
P. aeruginosa
strains have diverged from other isolates and form a distinct cluster based on MLST and phylogenetic analyses of seven housekeeping genes.
Inducible RNA Interference of
brlA
β in
Aspergillus nidulans
Authors: Barton L. M. , Prade R. A.
Published: August 2008

An inducible RNA interference (RNAi) construct composed of inverted repeating
alcA
promoters flanking the developmental regulatory gene
brlA
β was tested in
Aspergillus nidulans
. On inducing medium, the RNAi strains failed to sporulate and lacked
brlA
α and
brlA
β expression. RNAi was specific for
brlA
β, but not
brlA
α, silencing, indicating
brlA
α regulation by
brlA
β.
The Crucial Role of the Pls1 Tetraspanin during Ascospore Germination inPodospora anserinaProvides an Example of the Convergent Evolution of Morphogenetic Processes in Fungal Plant Pathogens and Saprobes
Authors: Lambou Karine , Malagnac Fabienne , Barbisan Crystel , Tharreau Didier , Lebrun Marc-Henri , Silar Philippe
Published: August 2008

Pls1 tetraspanins were shown for some pathogenic fungi to be essential for appressorium-mediated penetration into their host plants. We show here thatPodospora anserina, a saprobic fungus lacking appressorium, containsPaPls1, a gene orthologous to knownPLS1genes. Inactivation ofPaPls1demonstrates that this gene is specifically required for the germination of ascospores inP. anserina. These ascospores are heavily melanized cells that germinate under inducing conditions through a specific pore. On the contrary,MgPLS1, which fully complements a ΔPaPls1ascospore germination defect, has no role in the germination ofMagnaporthe griseanonmelanized ascospores but is required for the formation of the penetration peg at the pore of its melanized appressorium.P. anserinamutants with mutation ofPaNox2, which encodes the NADPH oxidase of the NOX2 family, display the same ascospore-specific germination defect as the ΔPaPls1mutant. Both mutant phenotypes are suppressed by the inhibition of melanin biosynthesis, suggesting that they are involved in the same cellular process required for the germination ofP. anserinamelanized ascospores. The analysis of the distribution ofPLS1andNOX2genes in fungal genomes shows that they are either both present or both absent. These results indicate that the germination ofP. anserinaascospores and the formation of theM. griseaappressorium penetration peg use the same molecular machinery that includes Pls1 and Nox2. This machinery is specifically required for the emergence of polarized hyphae from reinforced structures such as appressoria and ascospores. Its recurrent recruitment during fungal evolution may account for some of the morphogenetic convergence observed in fungi.
Systematic Identification and Sequence Analysis of the Genomic Islands of the EnteropathogenicEscherichia coliStrain B171-8 by the Combined Use of Whole-Genome PCR Scanning and Fosmid Mapping
Authors: Ogura Yoshitoshi , Abe Hiroyuki , Katsura Keisuke , Kurokawa Ken , Asadulghani Md , Iguchi Atsushi , Ooka Tadasuke , Nakayama Keisuke , Yamashita Atsushi , Hattori Masahira , Tobe Toru , Hayashi Tetsuya
Published: August 2008

EnteropathogenicEscherichia coli(EPEC) and enterohemorrhagicE. coli(EHEC) are diarrheagenic pathogens that colonize the intestinal tract through the formation of attaching and effacing lesions, induced by effectors translocated via a type III secretion system (T3SS) encoded on the locus of enterocyte effacement (LEE). In EHEC O157, numerous virulence factors, including around 40 T3SS effectors, have been identified. Most of them are encoded on genomic islands (GEIs) such as prophages and integrative elements. For EPEC, however, no systematic search of GEIs and virulence-related genes carried therein has been done, and only a limited number of virulence factors have been identified so far. In this study, we performed a systemic and genome-wide survey of the GEIs in strain B171-8, one of the prototype strains of EPEC, by the combined use of whole-genome PCR scanning and fosmid mapping and identified 22 large GEIs, including nine lambda-like prophages, three P2-like prophages, the LEE, and three additional integrative elements. On these prophages and integrative elements, we found genes for a set of T3SS proteins, a total of 33 T3SS effectors or effector homologues, and 12 other virulence factors which include five nonfimbrial adhesins. Most of the T3SS effector families identified are also present in EHEC O157, but B171-8 possesses a significantly smaller number of effectors. Not only the presence or absence of Shiga toxin genes but also the difference in the T3SS effector repertoire should be considered in analyzing the pathogenicity of EPEC and EHEC strains.
Deciphering the Unusual Acylation Pattern of
Helicobacter pylori
Lipid A
Authors: Stead Christopher M. , Beasley Ashley , Cotter Robert J. , Trent M. Stephen
Published: August 2008

The synthesis of “typical” hexa-acylated lipid A occurs via a nine-step enzymatic pathway, which is generally well conserved throughout all gram-negative bacteria. One exception to the rule is
Helicobacter pylori
, which has only eight homologs to the nine lipid A biosynthetic enzymes. The discrepancy occurs toward the end of the pathway, with
H. pylori
containing only a single putative secondary acyltransferase encoded by jhp0265. In
Escherichia coli
K-12, two late acyltransferases, termed LpxL and LpxM, are required for the biosynthesis of hexa-acylated lipid A. Detailed biochemical and genetic analyses reveal that
H. pylori
Jhp0265 (the protein encoded by jhp0265) is in fact an LpxL homolog, capable of transferring a stearoyl group to the hydroxyl group of the 2′ linked fatty acyl chain of lipid A. Despite the lack of a homolog to LpxM in the
H. pylori
genome, the organism synthesizes a hexa-acylated lipid A species, suggesting that an equivalent enzyme exists. Using radiolabeled lipid A substrates and acyl-acyl carrier protein as the fatty acyl donor, we were able to confirm the presence of a second
H. pylori
late acyl transferase by biochemical assays. After synthesis of the hexa-acylated lipid A species, several modification enzymes then function to produce the major lipid A species of
H. pylori
that is tetra-acylated. Jhp0634 was identified as an outer membrane deacylase that removes the 3′-linked acyl chains of
H. pylori
lipid A. Together, this work elucidates the biochemical machinery required for the acylation and deacylation of the lipid A domain of
H. pylori
lipopolysaccharide.
TheMycobacterium tuberculosis phoPROperon Is Positively Autoregulated in the Virulent Strain H37Rv
Authors: Gonzalo-Asensio Jesús , Soto Carlos Y. , Arbués Ainhoa , Sancho Javier , del Carmen Menéndez María , García María J. , Gicquel Brigitte , Martín Carlos
Published: August 2008

The attenuatedMycobacterium tuberculosisH37Ra strain is an isogenic counterpart of the virulent paradigm strain H37Rv. Recently, a link between a point mutation in the PhoP transcriptional regulator and avirulence of H37Ra was established. Remarkably, a previous study demonstrated negative autoregulation of thephoPgene in H37Ra. These findings led us to study the transcriptional autoregulation of PhoP in the virulent H37Rv strain. In contrast to the negative autoregulation of PhoP previously published for H37Ra, our experiments using aphoPpromoter-lacZfusion showed that PhoP is positively autoregulated in both H37Rv and H37Ra compared with an H37RvphoPdeletion mutant constructed in this study. Using quantitative reverse transcription-PCR (RT-PCR) analysis, we showed that thephoPgene is transcribed at similar levels in H37Rv and H37Ra. Gel mobility shift and DNase I footprinting assays allowed us to identify the precise binding region of PhoP from H37Rv to thephoPpromoter. We also carried out RT-PCR studies to demonstrate thatphoPis transcribed together with the adjacent genephoR, which codes for the cognate histidine kinase of thephoPRtwo-component system. In addition, quantitative RT-PCR studies showed thatphoRis independently transcribed from a promoter possibly regulated by PhoP. Finally, we discuss the possible role in virulence of a single point mutation found in thephoPgene from the attenuated H37Ra strain but not in virulent members of theM. tuberculosiscomplex.
A Soluble NADH-Dependent Fumarate Reductase in the Reductive Tricarboxylic Acid Cycle of
Hydrogenobacter thermophilus
TK-6
Authors: Miura Akane , Kameya Masafumi , Arai Hiroyuki , Ishii Masaharu , Igarashi Yasuo
Published: August 2008

Fumarate reductase (FRD) is an enzyme that reduces fumarate to succinate. In many organisms, it is bound to the membrane and uses electron donors such as quinol. In this study, an FRD from a thermophilic chemolithoautotrophic bacterium,
Hydrogenobacter thermophilus
TK-6, was purified and characterized. FRD activity using NADH as an electron donor was not detected in the membrane fraction but was found in the soluble fraction. The purified enzyme was demonstrated to be a novel type of FRD, consisting of five subunits. One subunit showed high sequence identity to the catalytic subunits of known FRDs. Although the genes of typical FRDs are assembled in a cluster, the five genes encoding the
H. thermophilus
FRD were distant from each other in the genome. Furthermore, phylogenetic analysis showed that the
H. thermophilus
FRD was located in a distinct position from those of known soluble FRDs. This is the first report of a soluble NADH-dependent FRD in
Bacteria
and of the purification of a FRD that operates in the reductive tricarboxylic acid cycle.
Evolutionary Comparison of Ribosomal Operon Antitermination Function
Authors: Arnvig Kristine B. , Zeng Shirley , Quan Selwyn , Papageorge Alexander , Zhang Ning , Villapakkam Anuradha C. , Squires Catherine L.
Published: August 2008

Transcription antitermination in the ribosomal operons of
Escherichia coli
results in the modification of RNA polymerase by specific proteins, altering its basic properties. For such alterations to occur, signal sequences in
rrn
operons are required as well as individual interacting proteins. In this study we tested putative
rrn
transcription antitermination-inducing sequences from five different bacteria for their abilities to function in
E. coli
. We further examined their response to the lack of one known
rrn
transcription antitermination protein from
E. coli
, NusB. We monitored antitermination activity by assessing the ability of RNA polymerase to read through a factor-dependent terminator. We found that, in general, the closer the regulatory sequence matched that of
E. coli
, the more likely there was to be a successful antitermination-proficient modification of the transcription complex. The
rrn
leader sequences from
Pseudomonas aeruginosa
,
Bacillus subtilis
, and
Caulobacter crescentus
all provided various levels of, but functionally significant antitermination properties to, RNA polymerase, while those of
Mycobacterium tuberculosis
and
Thermotoga maritima
did not. Possible RNA folding structures of presumed antitermination sequences and specific critical bases are discussed in light of our results. An unexpected finding was that when using the
Caulobacter crescentus rrn
leader sequence, there was little effect on terminator readthrough in the absence of NusB. All other hybrid antitermination system activities required this factor. Possible reasons for this finding are discussed.
Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a
Pseudomonas aeruginosa
Isolate in Mammals
Authors: Battle Scott E. , Meyer Folker , Rello Jordi , Kung Vanderlene L. , Hauser Alan R.
Published: August 2008

Most known virulence determinants of
Pseudomonas aeruginosa
are remarkably conserved in this bacterium's core genome, yet individual strains differ significantly in virulence. One explanation for this discrepancy is that pathogenicity islands, regions of DNA found in some strains but not in others, contribute to the overall virulence of
P. aeruginosa.
Here we employed a strategy in which the virulence of a panel of
P. aeruginosa
isolates was tested in mouse and plant models of disease, and a highly virulent isolate, PSE9, was chosen for comparison by subtractive hybridization to a less virulent strain, PAO1. The resulting subtractive hybridization sequences were used as tags to identify genomic islands found in PSE9 but absent in PAO1. One 99-kb island, designated
P. aeruginosa
genomic island 5 (PAGI-5), was a hybrid of the known
P. aeruginosa
island PAPI-1 and novel sequences. Whereas the PAPI-1-like sequences were found in most tested isolates, the novel sequences were found only in the most virulent isolates. Deletional analysis confirmed that some of these novel sequences contributed to the highly virulent phenotype of PSE9. These results indicate that targeting highly virulent strains of
P. aeruginosa
may be a useful strategy for identifying pathogenicity islands and novel virulence determinants.
Oms38 Is the First Identified Pore-Forming Protein in the Outer Membrane of Relapsing Fever Spirochetes
Authors: Thein Marcus , Bunikis Ignas , Denker Katrin , Larsson Christer , Cutler Sally , Drancourt Michel , Schwan Tom G. , Mentele Reinhard , Lottspeich Friedrich , Bergström Sven , Benz Roland
Published: August 2008

Relapsing fever is a worldwide, endemic disease caused by several spirochetal species belonging to the genus
Borrelia
. During the recurring fever peaks, borreliae proliferate remarkably quickly compared to the slow dissemination of Lyme disease
Borrelia
and therefore require efficient nutrient uptake from the blood of their hosts. This study describes the identification and characterization of the first relapsing fever porin, which is present in the outer membranes of
B. duttonii
,
B. hermsii
,
B. recurrentis
, and
B. turicatae
. The pore-forming protein was purified by hydroxyapatite chromatography and designated Oms38, for outer membrane-spanning protein of 38 kDa. Biophysical characterization of Oms38 was done by using the black lipid bilayer method, demonstrating that Oms38 forms small, water-filled channels of 80 pS in 1 M KCl that did not exhibit voltage-dependent closure. The Oms38 channel is slightly selective for anions and shows a ratio of permeability for cations over anions of 0.41 in KCl. Analysis of the deduced amino acid sequences demonstrated that Oms38 contains an N-terminal signal sequence which is processed under in vivo conditions. Oms38 is highly conserved within the four studied relapsing fever species, sharing an overall amino acid identity of 58% and with a strong indication for the presence of amphipathic β-sheets.
THE AZIMUTH STRUCTURE OF NUCLEAR COLLISIONS — I
Authors: TRAINOR THOMAS A. , KETTLER DAVID T.
Published: August 2008

We describe azimuth structure commonly associated with elliptic and directed flow in the context of 2D angular autocorrelations for the purpose of precise separation of so-called nonflow (mainly minijets) from flow. We extend the Fourier-transform description of azimuth structure to include power spectra and autocorrelations related by the Wiener–Khintchine theorem. We analyze several examples of conventional flow analysis in that context and question the relevance of reaction plane estimation to flow analysis. We introduce the 2D angular autocorrelation with examples from data analysis and describe a simulation exercise which demonstrates precise separation of flow and nonflow using the 2D autocorrelation method. We show that an alternative correlation measure based on Pearson's normalized covariance provides a more intuitive measure of azimuth structure.
A NOVEL SOFTWARE-BUILT PARALLEL MACHINES AND THEIR INTERCONNECTIONS
Authors: AKON MOHAMMAD MURSALIN , GOSWAMI DHRUBAJYOTI , LI HON FUNG , SHEN XUEMIN (SHERMAN) , SINGH AJIT
Published: August 2008

In this paper, we introduce SPM (Software-built Parallel Machines), a model to create software based virtual parallel machines. With SPM, an application developer simply selects all the required virtual parallel machines from the repository and implements the intended parallel algorithms directly without any need of complex mappings, as if the required processor interconnections are readily available. In addition, we present an implementation of the SPM model, which provides a systematic way to design new virtual machines. Our experiments show that the applications developed using the SPM model and tools give excellent performance, as compared to the applications developed using a generic communication library, such as MPI.
CONTROLLING CIOQ SWITCHES WITH PRIORITY QUEUING AND IN MULTISTAGE INTERCONNECTION NETWORKS
Authors: KESSELMAN ALEX , ROSÉN ADI
Published: August 2008

Combined input and output queued (CIOQ) architectures with a moderate fabric speedupS > 1 have come to play a major role in the design of high performance switches. In this paper we study CIOQ switches in two settings. The first is a setting of a single CIOQ switch with Priority Queuing (PQ) buffers, which provide better Quality of Service (QoS) guarantees by decreasing the delay experienced by mission-critical and real-time traffic. The second is a setting of a Multistage Interconnection Network (MIN), where each Switching Element (SE) is a CIOQ switch. In the first setting, we consider the case of traffic with packets having variable values. The goal of the switch policy is to maximize the total value of packets sent out of the switch. We present a switch policy that is 6-competitive for any speedup. In the second setting, we study a MIN architecture in which each internal buffer is further divided into virtual buffers, one per each MIN output port reachable from that buffer. We consider the case of traffic with unit value packets, and the goal of the policy managing the MIN is to maximize the total number of packets sent out of the MIN. We give a local memoryless switch policy that uses back pressure and achieves a competitive ratio of (4h + 1), where h is the number of stages of the MIN. The proposed policy is simple and can be efficiently implemented at high speeds. We also demonstrate a lower bound of h/2 on the competitive ratio of any local work-conserving deterministic memoryless switch policy. We further show that without back pressure, no online local work-conserving deterministic switch policy can break the competitive ratio of [Formula: see text], where N is the size of the MIN and k is the size of an SE.
Aerobic conditioning and allergic pulmonary inflammation in mice. II. Effects on lung vascular and parenchymal inflammation and remodeling
Authors: Vieira Rodolfo P. , de Andrade Vanessa F. , Duarte Anna Cecília S. , dos Santos Ângela B. G. , Mauad Thaís , Martins Milton A. , Dolhnikoff Marisa , Carvalho Celso R. F.
Published: August 2008

Recent evidence suggests that asthma leads to inflammation and remodeling not only in the airways but also in pulmonary vessels and parenchyma. In addition, some studies demonstrated that aerobic training decreases chronic allergic inflammation in the airways; however, its effects on the pulmonary vessels and parenchyma have not been previously evaluated. Our objective was to test the hypothesis that aerobic conditioning reduces inflammation and remodeling in pulmonary vessels and parenchyma in a model of chronic allergic lung inflammation. Balb/c mice were sensitized at days 0, 14, 28, and 42 and challenged with ovalbumin (OVA) from day 21 to day 50. Aerobic training started on day 21 and continued until day 50. Pulmonary vessel and parenchyma inflammation and remodeling were evaluated by quantitative analysis of eosinophils and mononuclear cells and by collagen and elastin contents and smooth muscle thickness. Immunohistochemistry was performed to quantify the density of positive cells to interleukin (IL)-2, IL-4, IL-5, interferon-γ, IL-10, monocyte chemotatic protein (MCP)-1, nuclear factor (NF)-κB p65, and insulin-like growth factor (IGF)-I. OVA exposure induced pulmonary blood vessels and parenchyma inflammation as well as increased expression of IL-4, IL-5, MCP-1, NF-κB p65, and IGF-I by inflammatory cells were reduced by aerobic conditioning. OVA exposure also induced an increase in smooth muscle thickness and elastic and collagen contents in pulmonary vessels, which were reduced by aerobic conditioning. Aerobic conditioning increased the expression of IL-10 in sensitized mice. We conclude that aerobic conditioning decreases pulmonary vascular and parenchymal inflammation and remodeling in this experimental model of chronic allergic lung inflammation in mice.
CRTH2 antagonism significantly ameliorates airway hyperreactivity and downregulates inflammation-induced genes in a mouse model of airway inflammation
Authors: Lukacs Nicholas W. , Berlin Aaron A. , Franz-Bacon Karin , Šášik Roman , Sprague L. James , Ly Tai Wei , Hardiman Gary , Boehme Stefen A. , Bacon Kevin B.
Published: August 2008

Prostaglandin D2, the ligand for the G protein-coupled receptors DP1 and CRTH2, has been implicated in the pathogenesis of the allergic response in diseases such as asthma, rhinitis, and atopic dermatitis. This prostanoid also fulfills a number of physiological, anti-inflammatory roles through its receptor DP1. We investigated the role of PGD2and CRTH2 in allergic pulmonary inflammation by using a highly potent and specific antagonist of CRTH2. Administration of this antagonist ameliorated inflammation caused by either acute or subchronic sensitization using the cockroach egg antigen. Gene expression and ELISA analysis revealed that there was reduced proinflammatory cytokine mRNA or protein produced, as well as a wide array of genes associated with the Th2-type proinflammatory response. Importantly, the CRTH2 antagonist reduced antigen-specific IgE, IgG1, and IgG2a antibody levels as well as decreased mucus deposition and leukocyte infiltration in the large airways. Collectively, these findings suggest that the PGD2-CRTH2 activation axis has a pivotal role in mediating the inflammation and the underlying immune response in a T cell-driven model of allergic airway inflammation.
Lack of potentiating effect of increasing temperature on responses to chemical activators in vagal sensory neurons isolated from TRPV1-null mice
Authors: Ni Dan , Lee Lu-Yuan
Published: August 2008

Our recent study (Ni D, Lee LY. Am J Physiol Lung Cell Mol Physiol 294: L563–L571, 2008) demonstrated that the responses of rat pulmonary sensory neurons to transient receptor potential vanilloid (TRPV)1 activators were enhanced by increasing temperature, but the role of the TPRV1 channel in this potentiating effect could not be definitively evaluated. In the present study, we used whole cell perforated patch-clamp technique to compare the responses of isolated nodose/jugular sensory neurons to chemical activators and increasing temperature between wild-type (WT) and TRPV1-null (TRPV1−/−) mice. Our results showed that, in voltage-clamp mode, the peak inward current evoked by hyperthermia was not different between WT and TRPV1−/− neurons; however, the inward current evoked by 2-aminoethoxydiphenyl borate (2-APB), a common activator of TRPV1–3 channels, was greatly potentiated by increasing temperature from 36 to 40.5°C in WT neurons ( n = 9; P < 0.01) but was not affected by the same change in temperature in TRPV1−/− neurons ( n = 9; P = 0.54). Similarly, the inward current evoked by acid (pH 5.5), an activator of both TRPV1 channel and the acid-sensing ion channel, was enhanced by increasing temperature ( n = 7; P < 0.05) in WT neurons, and this potentiating effect was absent in TRPV1−/− neurons ( n = 13; P = 0.11). These results demonstrated that deletion of the TRPV1 channel does not significantly alter the stimulatory effect of hyperthermia on nodose/jugular neurons but eliminates the potentiating effect of increasing temperature on the responses of these neurons to nonselective TRPV1 channel activators. This study further suggests that a positive interaction between these chemical activators and increasing temperature at the TRPV1 channel is primarily responsible for the hyperthermia-induced sensitization of these neurons.
Nonexistence of NdMMgMn2O6 (M=Li, Na, K, Cs) compounds
Authors: Nalbandyan V. B.
Published: August 2008

Reported results for four new cubic compounds NdMMgMn2O6 (M=Li, Na, K, Cs) are questionable and cast doubt on the existence of such compounds. The lattice constants and relative intensities are essentially the same regardless of the nature of M; the X-ray diffraction patterns may be indexed with the lattice constants divided by √8, which result in much better figures of merit and a=0.3861 to 0.3883 nm, close to the subcell parameter of non-stoichiometric pseudocubic NdMnO3.
X-ray powder diffraction data for Al73.5Ni18.5Re8 orthorhombic phase
Authors: Grushko B. , Balanetskyy S.
Published: August 2008

A ternary phase was revealed in Al-Ni-Re in a small compositional range around Al73.5Ni18.5Re8. Using powder X-ray diffraction and electron diffraction, it was found to have an orthorhombic structure with a=10.048(3) Å, b=15.423(8) Å, and c=8.367(3) Å.
Investigation of Neolithic ceramic pigments using synchrotron radiation X-ray diffraction
Authors: Bugoi Roxana , Constantinescu Bogdan , Pantos Emmanuel , Popovici Dragomir
Published: August 2008

Crystalline phases present in pigments scratched off the surfaces of some decorated ceramic sherds belonging to the Cucuteni Neolithic culture were successfully identified using synchrotron radiation X-ray diffraction at Daresbury Laboratory. The ceramic sherds were selected from a collection of the National Museum of Romanian History in Bucharest. The synchrotron radiation X-ray diffraction analysis revealed that the black-color pigments on the surface of a number of sherds were produced by a variety of jacobsite (Fe2MnO4) phases; magnetite (Fe3O4) was also found in one of the sherds. The red color was derived from clay slips with a high content of hematite (Fe2O3). Calcite (CaCO3) was found in the white pigments; its presence was explained as being related to postburial deposition processes. Conclusions on technological aspects, provenance, and conservation issues are given.
X-ray powder diffraction data for ErH2−xDx
Authors: Rodriguez Mark A. , Ferrizz Robert M. , Snow Clark S. , Browning James F.
Published: August 2008

X-ray powder diffraction data for ErH2−xDx formed by hydrogen (i.e., protium)–deuterium loading of Er metal are reported. Lattice parameters for the varying hydrogen–deuterium compositions followed Vergard’s law behavior. The cubic lattice parameter at room temperature for ErH2−xDx obeys a linear relationship according to the formula a=5.1287−1.1120×10−4⋅x, where a is the lattice parameter of the fluorite-type structure and x is the mole percent of deuterium. Microstrain measurements suggest a possible ordering of hydrogen and deuterium in the composition ErH1D1.
Corrections to “Thermal expansion of anatase and rutile between 300 and 575 K using synchrotron powder X-ray diffraction” [Powder Diffr. 22, 352–357 (2007)]
Authors: Hummer D. R. , Heaney P. J. , Post J. E.
Published: August 2008

Corrections are made to two equations and one table value in “Thermal expansion of anatase and rutile between 300 and 575 K using synchrotron powder X-ray diffraction” [Powder Diffr. 22, 352–357 (2007)].