bluuebunny/crossref_metadata_2025 huggingface dataset:
Analyses of Current-Generating Mechanisms of
Shewanella loihica
PV-4 and
Shewanella oneidensis
MR-1 in Microbial Fuel Cells
Authors: Newton Gregory J. , Mori Shigeki , Nakamura Ryuhei , Hashimoto Kazuhito , Watanabe Kazuya
Published: October 2009

Although members of the genus
Shewanella
have common features (e.g., the presence of decaheme
c
-type cytochromes [
c
-cyts]), they are widely variable in genetic and physiological features. The present study compared the current-generating ability of
S. loihica
PV-4 in microbial fuel cells (MFCs) with that of well-characterized
S. oneidensis
MR-1 and examined the roles of
c
-cyts in extracellular electron transfer. We found that strains PV-4 and MR-1 exhibited notable differences in current-generating mechanisms. While the MR-1 MFCs maintained a constant current density over time, the PV-4 MFCs continued to increase in current density and finally surpassed the MR-1 MFCs. Coulombic efficiencies reached 26% in the PV-4 MFC but 16% in the MR-1 MFCs. Although both organisms produced quinone-like compounds, anode exchange experiments showed that anode-attached cells of PV-4 produced sevenfold more current than planktonic cells in the same chamber, while planktonic cells of MR-1 produced twice the current of the anode-attached cells. Examination of the genome sequence indicated that PV-4 has more
c
-cyt genes in the metal reductase-containing locus than MR-1. Mutational analysis revealed that PV-4 relied predominantly on a homologue of the decaheme
c
-cyt MtrC in MR-1 for current generation, even though it also possesses two homologues of the decaheme
c
-cyt OmcA in MR-1. These results suggest that current generation in a PV-4 MFC is in large part accomplished by anode-attached cells, in which the MtrC homologue constitutes the main path of electrons toward the anode.
Genetic Features of Resident Biofilms Determine Attachment of
Listeria monocytogenes
Authors: Habimana Olivier , Meyrand Mickael , Meylheuc Thierry , Kulakauskas Saulius , Briandet Romain
Published: October 2009

Planktonic
Listeria monocytogenes
cells in food-processing environments tend most frequently to adhere to solid surfaces. Under these conditions, they are likely to encounter resident biofilms rather than a raw solid surface. Although metabolic interactions between
L. monocytogenes
and resident microflora have been widely studied, little is known about the biofilm properties that influence the initial fixation of
L. monocytogenes
to the biofilm interface. To study these properties, we created a set of model resident
Lactococcus lactis
biofilms with various architectures, types of matrices, and individual cell surface properties. This was achieved using cell wall mutants that affect bacterial chain formation, exopolysaccharide (EPS) synthesis and surface hydrophobicity. The dynamics of the formation of these biofilm structures were analyzed in flow cell chambers using in situ time course confocal laser scanning microscopy imaging. All the
L. lactis
biofilms tested reduced the initial immobilization of
L. monocytogenes
compared to the glass substratum of the flow cell. Significant differences were seen in
L. monocytogenes
settlement as a function of the genetic background of resident lactococcal biofilm cells. In particular, biofilms of the
L. lactis
chain-forming mutant resulted in a marked increase in
L. monocytogenes
settlement, while biofilms of the EPS-secreting mutant efficiently prevented pathogen fixation. These results offer new insights into the role of resident biofilms in governing the settlement of pathogens on food chain surfaces and could be of relevance in the field of food safety controls.
Microbial Production of Glyceric Acid, an Organic Acid That Can Be Mass Produced from Glycerol
Authors: Habe Hiroshi , Shimada Yuko , Yakushi Toshiharu , Hattori Hiromi , Ano Yoshitaka , Fukuoka Tokuma , Kitamoto Dai , Itagaki Masayuki , Watanabe Kunihiro , Yanagishita Hiroshi , Matsushita Kazunobu , Sakaki Keiji
Published: October 2009

Glyceric acid (GA), an unfamiliar biotechnological product, is currently produced as a small by-product of dihydroxyacetone production from glycerol by
Gluconobacter oxydans
. We developed a method for the efficient biotechnological production of GA as a target compound for new surplus glycerol applications in the biodiesel and oleochemical industries. We investigated the ability of 162 acetic acid bacterial strains to produce GA from glycerol and found that the patterns of productivity and enantiomeric GA compositions obtained from several strains differed significantly. The growth parameters of two different strain types,
Gluconobacter frateurii
NBRC103465 and
Acetobacter tropicalis
NBRC16470, were optimized using a jar fermentor.
G. frateurii
accumulated 136.5 g/liter of GA with a 72%
d
-GA enantiomeric excess (ee) in the culture broth, whereas
A. tropicalis
produced 101.8 g/liter of
d
-GA with a 99% ee. The 136.5 g/liter of glycerate in the culture broth was concentrated to 236.5 g/liter by desalting electrodialysis during the 140-min operating time, and then, from 50 ml of the concentrated solution, 9.35 g of GA calcium salt was obtained by crystallization. Gene disruption analysis using
G. oxydans
IFO12528 revealed that the membrane-bound alcohol dehydrogenase (mADH)-encoding gene (
adhA
) is required for GA production, and purified mADH from
G. oxydans
IFO12528 catalyzed the oxidation of glycerol. These results strongly suggest that mADH is involved in GA production by acetic acid bacteria. We propose that GA is potentially mass producible from glycerol feedstock by a biotechnological process.
Importance of Polyphosphate Kinase 1 for
Campylobacter jejuni
Viable-but-Nonculturable Cell Formation, Natural Transformation, and Antimicrobial Resistance
Authors: Gangaiah Dharanesh , Kassem Issmat I. , Liu Zhe , Rajashekara Gireesh
Published: October 2009

Campylobacter jejuni
, a gram-negative, microaerophilic bacterium, is a predominant cause of bacterial gastroenteritis in humans. Although considered fragile and fastidious and lacking many classical stress response mechanisms,
C
.
jejuni
exhibits a remarkable capacity for survival and adaptation, successfully infecting humans and persisting in the environment. Consequently, understanding the physiological and genetic properties that allow
C
.
jejuni
to survive and adapt to various stress conditions is crucial for therapeutic interventions. Of importance is polyphosphate (poly-P) kinase 1 (PPK1), which is a key enzyme mediating the synthesis of poly-P, an essential molecule for survival, mediating stress responses, host colonization, and virulence in many bacteria. Therefore, we investigated the role of PPK1 in
C
.
jejuni
pathogenesis, stress survival, and adaptation. Our findings demonstrate that a
C
.
jejuni
Δ
ppk1
mutant was deficient in poly-P accumulation, which was associated with a decreased ability to form viable-but-nonculturable cells under acid stress. The Δ
ppk1
mutant also showed a decreased frequency of natural transformation and an increased susceptibility to various antimicrobials. Furthermore, the Δ
ppk1
mutant was characterized by a dose-dependent deficiency in chicken colonization. Complementation of the Δ
ppk
1 mutant with the wild-type copy of
ppk1
restored the deficient phenotypes to levels similar to those of the wild type. Our results suggest that poly-P plays an important role in stress survival and adaptation and might contribute to genome plasticity and the spread and development of antimicrobial resistance in
C
.
jejuni
. These findings highlight the potential of PPK1 as a novel target for therapeutic interventions.
In Vivo Display of a Multisubunit Enzyme Complex on Biogenic Magnetic Nanoparticles
Authors: Ohuchi Shoji , Schüler Dirk
Published: October 2009

Magnetosomes are unique bacterial organelles comprising membrane-enveloped magnetic crystals produced by magnetotactic bacteria. Because of several desirable chemical and physical properties, magnetosomes would be ideal scaffolds on which to display highly complicated biological complexes artificially. As a model experiment for the functional expression of a multisubunit complex on magnetosomes, we examined the display of a chimeric bacterial RNase P enzyme composed of the protein subunit (C5) of
Escherichia coli
RNase P and the endogenous RNA subunit by expressing a translational fusion of C5 with MamC, a known magnetosome protein, in the magnetotactic bacterium
Magnetospirillum gryphiswaldense
. As intended, the purified C5 fusion magnetosomes, but not wild-type magnetosomes, showed apparent RNase P activity and the association of a typical bacterial RNase P RNA. Our results demonstrate for the first time that magnetosomes can be employed as scaffolds for the display of multisubunit complexes.
Reengineering
Escherichia coli
for Succinate Production in Mineral Salts Medium
Authors: Zhang X. , Jantama K. , Shanmugam K. T. , Ingram L. O.
Published: October 2009

The fermentative metabolism of glucose was redirected to succinate as the primary product without mutating any genes encoding the native mixed-acid fermentation pathway or redox reactions. Two changes in peripheral pathways were together found to increase succinate yield fivefold: (i) increased expression of phosphoenolpyruvate carboxykinase and (ii) inactivation of the glucose phosphoenolpyruvate-dependent phosphotransferase system. These two changes increased net ATP production, increased the pool of phosphoenolpyruvate available for carboxylation, and increased succinate production. Modest further improvements in succinate yield were made by inactivating the
pflB
gene, encoding pyruvate formate lyase, resulting in an
E
scherichia coli
pathway that is functionally similar to the native pathway in
Actinobacillus succinogenes
and other succinate-producing rumen bacteria.
Periplasmic Electron Transfer via the
c
-Type Cytochromes MtrA and FccA of
Shewanella oneidensis
MR-1
Authors: Schuetz Bjoern , Schicklberger Marcus , Kuermann Johannes , Spormann Alfred M. , Gescher Johannes
Published: October 2009

Dissimilatory microbial reduction of insoluble Fe(III) oxides is a geochemically and ecologically important process which involves the transfer of cellular, respiratory electrons from the cytoplasmic membrane to insoluble, extracellular, mineral-phase electron acceptors. In this paper evidence is provided for the function of the periplasmic fumarate reductase FccA and the decaheme
c
-type cytochrome MtrA in periplasmic electron transfer reactions in the gammaproteobacterium
Shewanella oneidensis
. Both proteins are abundant in the periplasm of ferric citrate-reducing
S. oneidensis
cells. In vitro fumarate reductase FccA and
c
-type cytochrome MtrA were reduced by the cytoplasmic membrane-bound protein CymA. Electron transfer between CymA and MtrA was 1.4-fold faster than the CymA-catalyzed reduction of FccA. Further experiments showing a bidirectional electron transfer between FccA and MtrA provided evidence for an electron transfer network in the periplasmic space of
S. oneidensis
. Hence, FccA could function in both the electron transport to fumarate and via MtrA to mineral-phase Fe(III). Growth experiments with a Δ
fccA
deletion mutant suggest a role of FccA as a transient electron storage protein.
Functional Genomic Analysis of Two
Staphylococcus aureus
Phages Isolated from the Dairy Environment
Authors: García Pilar , Martínez Beatriz , Obeso José María , Lavigne Rob , Lurz Rudi , Rodríguez Ana
Published: October 2009

The genomes of the two lytic mutant
Staphylococcus aureus
bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (
cos
) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the
S. aureus
-infecting phages.
Bacterial Polyester Inclusions Engineered To Display Vaccine Candidate Antigens for Use as a Novel Class of Safe and Efficient Vaccine Delivery Agents
Authors: Parlane Natalie A. , Wedlock D. Neil , Buddle Bryce M. , Rehm Bernd H. A.
Published: October 2009

Bioengineered bacterial polyester inclusions have the potential to be used as a vaccine delivery system. The biopolyester beads were engineered to display a fusion protein of the polyester synthase PhaC and the two key antigens involved in immune response to the infectious agent that causes tuberculosis,Mycobacterium tuberculosis, notably antigen 85A (Ag85A) and the 6-kDa early secreted antigenic target (ESAT-6) fromMycobacterium tuberculosis. Polyester beads displaying the respective fusion protein at a high density were successfully produced (henceforth called Ag85A-ESAT-6 beads) by recombinantEscherichia coli. The ability of the Ag85A-ESAT-6 beads to enhance mouse immunity to the displayed antigens was investigated. The beads were not toxic to the animals, as determined by weight gain and absence of lesions at the inoculation site in immunized animals. In vivo injection of the Ag85A-ESAT-6 beads in mice induced significant humoral and cell-mediated immune responses to both Ag85A and ESAT-6. Vaccination with Ag85A-ESAT-6 beads was efficient at stimulating immunity on their own, and this ability was enhanced by administration of the beads in an oil-in-water emulsion. In addition, vaccination with the Ag85A-ESAT-6 beads induced significantly stronger humoral and cell-mediated immune responses than vaccination with an equivalent dose of the fusion protein Ag85A-ESAT-6 alone. The immune response induced by the beads was of a mixed Th1/Th2 nature, as assessed from the induction of the cytokine gamma interferon (Th1 immune response) and increased levels of immunoglobulin G1 (Th2 immune response). Hence, engineered biopolyester beads displaying foreign antigens represent a new class of versatile, safe, and biocompatible vaccines.
Hwp1 and Related Adhesins Contribute to both Mating and Biofilm Formation in
Candida albicans
Authors: Ene Iuliana V. , Bennett Richard J.
Published: October 2009

Candida albicans
Hwp1, Hwp2, and Rbt1 are related cell wall proteins expressed during the programs of sexual differentiation and filamentous growth. In this study, we compare strains lacking either single factors or a combination of these genes, and we demonstrate distinct but overlapping roles in mating and biofilm formation.
The InhA Metalloproteases ofBacillus cereusContribute Concomitantly to Virulence
Authors: Guillemet Elisabeth , Cadot Céline , Tran Seav-Ly , Guinebretière Marie-Hélène , Lereclus Didier , Ramarao Nalini
Published: October 2009

The virulence ofBacillus cereusrequires that bacteria have the capacity to colonize their host, degrade specific tissues, and circumvent the host immune system. To study this aspect of pathogenesis, we focused on three metalloproteases, InhA1, InhA2, and InhA3, which share more than 66% identity. The expression of these metalloprotease genes was assessed by transcriptional fusions with alacZreporter gene. The expression profiles suggest a complementary time course of InhA production. Indeed, the genes are simultaneously expressed but are oppositely controlled during stationary phase. We constructed single and multipleinhAmutants and assessed the bacterial locations of the proteins as well as their individual or additive roles in macrophage escape and toxicity, antibacterial-peptide cleavage, and virulence. InhA1, a major component of the spore exosporium, is the only InhA metalloprotease involved in bacterial escape from macrophages. A mutant lackinginhA1,inhA2, andinhA3shows a strong decrease in the level of virulence for insects. Taken together, these results show that the InhA metalloproteases ofB. cereusare important virulence factors that may allow the bacteria to counteract the host immune system.
Outer Membrane Machinery and Alginate Synthesis Regulators Control Membrane Vesicle Production inPseudomonas aeruginosa
Authors: Tashiro Yosuke , Sakai Ryosuke , Toyofuku Masanori , Sawada Isao , Nakajima-Kambe Toshiaki , Uchiyama Hiroo , Nomura Nobuhiko
Published: October 2009

The opportunistic human bacterial pathogenPseudomonas aeruginosaproduces membrane vesicles (MVs) in its surrounding environment. Several features of theP. aeruginosaMV production mechanism are still unknown. We previously observed that depletion of Opr86, which has a role in outer membrane protein (OMP) assembly, resulted in hypervesiculation. In this study, we showed that the outer membrane machinery and alginate synthesis regulatory machinery are closely related to MV production inP. aeruginosa. Depletion of Opr86 resulted in increased expression of the periplasmic serine protease MucD, suggesting that the accumulation of misfolded OMPs in the periplasm is related to MV production. Indeed, themucDmutant showed a mucoid phenotype and themucDmutation caused increased MV production. Strains with the gene encoding alginate synthetic regulator AlgU, MucA, or MucB deleted also caused altered MV production. Overexpression of either MucD or AlgW serine proteases resulted in decreased MV production, suggesting that proteases localized in the periplasm repress MV production inP. aeruginosa. Deletion ofmucDresulted in increased MV proteins, even in strains with mutations in thePseudomonasquinolone signal (PQS), which serves as a positive regulator of MV production. This study suggests that misfolded OMPs may be important for MV production, in addition to PQS, and that these regulators act in independent pathways.
Diamide Triggers Mainly S Thiolations in the Cytoplasmic Proteomes of
Bacillus subtilis
and
Staphylococcus aureus
Authors: Pöther Dierk-Christoph , Liebeke Manuel , Hochgräfe Falko , Antelmann Haike , Becher Dörte , Lalk Michael , Lindequist Ulrike , Borovok Ilya , Cohen Gerald , Aharonowitz Yair , Hecker Michael
Published: October 2009

Glutathione constitutes a key player in the thiol redox buffer in many organisms. However, the gram-positive bacteria
Bacillus subtilis
and
Staphylococcus aureus
lack this low-molecular-weight thiol. Recently, we identified S-cysteinylated proteins in
B. subtilis
after treatment of cells with the disulfide-generating electrophile diamide. S cysteinylation is thought to protect protein thiols against irreversible oxidation to sulfinic and sulfonic acids. Here we show that S thiolation occurs also in
S. aureus
proteins after exposure to diamide. We further analyzed the formation of inter- and intramolecular disulfide bonds in cytoplasmic proteins using diagonal nonreducing/reducing sodium dodecyl sulfate gel electrophoresis. However, only a few proteins were identified that form inter- or intramolecular disulfide bonds under control and diamide stress conditions in
B. subtilis
and
S. aureus
. Depletion of the cysteine pool was concomitantly measured in
B. subtilis
using a metabolomics approach. Thus, the majority of reversible thiol modifications that were previously detected by two-dimensional gel fluorescence-based thiol modification assay are most likely based on S thiolations. Finally, we found that a glutathione-producing
B. subtilis
strain which expresses the
Listeria monocytogenes gshF
gene did not show enhanced oxidative stress resistance compared to the wild type.
An SOS-Regulated Type 2 Toxin-Antitoxin System
Authors: Singletary Larissa A. , Gibson Janet L. , Tanner Elizabeth J. , McKenzie Gregory J. , Lee Peter L. , Gonzalez Caleb , Rosenberg Susan M.
Published: October 2009

TheEscherichia colichromosome encodes seven demonstrated type 2 toxin-antitoxin (TA) systems: cassettes of two or three cotranscribed genes, one encoding a stable toxin protein that can cause cell stasis or death, another encoding a labile antitoxin protein, and sometimes a third regulatory protein. We demonstrate that theyafNOgenes constitute an additional chromosomal type 2 TA system that is upregulated during the SOS DNA damage response. TheyafNOPgenes are part of thedinBoperon, of whichdinBunderlies stress-induced mutagenesis mechanisms.yafNwas identified as a putative antitoxin by homology to known antitoxins, implicatingyafO(and/oryafP) as a putative toxin. Using phage-mediated cotransduction assays for linkage disruption, we show first thatyafNis an essential gene and second that it is essential only whenyafOis present. Third,yafPis not a necessary part of either the toxin or the antitoxin. Fourth, although DinB is required, theyafNOPgenes are not required for stress-induced mutagenesis in theEscherichia coliLac assay. These results imply thatyafNencodes an antitoxin that protects cells against ayafO-encoded toxin and show a protein-based TA system upregulated by the SOS response.
Polyphosphate Accumulation in
Escherichia coli
in Response to Defects in DNA Metabolism
Authors: Amado Luciana , Kuzminov Andrei
Published: October 2009

Phenol-chloroform extraction of [
32
P]orthophosphate-labeled
E
scherichia coli
cells followed by alkaline gel electrophoresis revealed, besides the expected chromosomal DNA, two non-DNA species that we have identified as lipopolysaccharides and polyphosphates by using a combination of biochemical and genetic techniques. We used this serendipitously found straightforward protocol for direct polyphosphate detection to quantify polyphosphate levels in
E. coli
mutants with diverse defects in the DNA metabolism. We detected increased polyphosphate accumulation in the
ligA
,
ligA recBCD
,
dut ung
, and
thyA
mutants. Polyphosphate accumulation may thus be an indicator of general DNA stress.
Nod2 regulates the host response towards microflora by modulating T cell function and epithelial permeability in mouse Peyer's patches
Authors: Barreau Frédérick , Madre Chrystèle , Meinzer Ulrich , Berrebi Dominique , Dussaillant Monique , Merlin Françoise , Eckmann Lars , Karin Mickael , Sterkers Ghislaine , Bonacorsi Stéphane , Lesuffleur Thécla , Hugot Jean-Pierre
Published: October 2009

Nucleotide oligomerisation domain 2 (NOD2) mutations are associated with susceptibility to Crohn's disease and graft-versus-host disease, two human disorders related with dysfunctions of Peyer's patches (PPs). In Nod2−/− mice transcellular permeability and bacterial translocation are increased in PPs. In this study, we show that both anti-CD4+ and anti-interferon γ (anti-IFNγ) monoclonal antibodies abrogate this phenotype and reduce the expression of tumour necrosis factor (TNF) receptor 2 and the long isoform of myosin light chain kinase, thus demonstrating that immune T cells influence the epithelial functions. In turn, intraperitoneal injection of ML-7 (a myosin light chain kinase inhibitor) normalises the values of CD4+ T cells, IFNγ and TNFα. This reciprocal cross-talk is under the control of the gut microflora as shown by the normalisation of all parameters after antibiotic treatment. Toll-like receptor 2 (TLR2) and TLR4 expression were increased in Nod2−/− mice under basal conditions and TLR2 and TLR4 agonists induced an increased transcellular permeability in Nod2+/+ mice. Muramyldipeptide (a Nod2 agonist) or ML-7 was able to reverse this phenomenon. It thus appears that Nod2 modulates the cross-talk between CD4+ T cells and the epithelium recovering PP and that it downregulates the pro-inflammatory effect driven by the ileal microflora, likely by inhibiting the TLR pathways.
Trophic Level Relationships in Pelagic Food Webs: Comparisons Derived from Long-Term Data Sets for Oneida Lake, New York (USA), and Lake St. George, Ontario (Canada)
Authors: McQueen Donald J. , Mills Edward L. , Forney John L. , Johannes Mark R. S. , Post John R.
Published: October 2009

We used standardized methods to analyze a 14-yr data set from Oneida Lake and a 10-yr data set from Lake St. George. We estimated mean summer concentrations of several trophic level indicators including piscivores, planktivores, zooplankton, phytoplankton, and total phosphorus, and we then investigated the relationships between these variables. Both data sets yielded similar long-term and short-term trends. The long-term mean annual trends were that (1) the relationships between concentrations of planktivores and zooplankton (including daphnids) were always negative, (2) the relationships between concentrations of zooplankton and various measures of phytoplankton abundance were unpredictable and never statistically significant, and (3) the relationships between total phosphorus and various measures of phytoplankton abundance were always positive. Over short periods, the data from both lakes showed periodic, strong top-down relationships between concentrations of zooplankton (especially large Daphnia) and chlorophyll a, but these events were unpredictable and were seldom related to piscivore abundance.
Hemolymph Ecdysone Concentration as a Function of Sexual Maturity in the Male Snow Crab (Chionoecetes opilio)
Authors: Cormier Roland J. , Fraser Alan R. , Bailey Richard F. J. , Raymond Nicole
Published: October 2009

Ecdysone concentrations in the hemolymph of juvenile and morphometrically mature male snow crab (Chionoecetes opilio) were determined by radioimmunoassay. A logarithmic transformation of the allometric relationship of the dry weight of the chelae versus the carapace width was used to identify morphometric maturity. Results indicate that concentrations of ecdysone found in the hemolymph of juvenile crab are higher than those found in morphometrically mature crab, thus providing a biochemical basis for the observation that the onset of sexual maturity seems to coincide with a terminal molt.
CONTROL OF WIND-INDUCED RESPONSE OF TRANSMISSION TOWER-LINE SYSTEM BY USING MAGNETORHEOLOGICAL DAMPERS
Authors: CHEN BO , ZHENG JIN , QU WEILIAN
Published: October 2009

Transmission tower-line system is a high-rise structure with low damping and it is therefore prone to strong wind excitation. In this paper, the control of wind-induced response of transmission tower-line system is carried out by using magnetorheological (MR) dampers. The effects of brace stiffness of damper are introduced and a multi-degree-of-freedom (MDOF) model is developed for both in-plane/out-of-plane vibration of transmission tower-line system. Two semi-active control strategies are proposed for the vibration mitigation of tower-line system. The first one is based on fixed increment of controllable damper force whereas the second one is a clipped-optimal strategy based on fuzzy control principle. The optimal parameters of the MDOF model of transmission line are investigated. A real transmission tower-line system constructed in China is taken as an example to examine the feasibility and reliability of the proposed approach. A parametric study is conducted for the effects of brace stiffness of MR damper, wind loading intensity, and parameters of MR fluids on the control performance. The results demonstrate that the incorporation of MR dampers into the transmission tower-line system can substantially suppress the wind-induced responses of transmission tower if the damper parameters are optimally determined. The performance of the two kinds of semi-active control approaches is better than that of a passive control approach.
ON THE CONNECTION FORMULAS OF THE FOURTH PAINLEVÉ TRANSCENDENT
Authors: WONG R. , ZHANG H. Y.
Published: October 2009

Using the method of "uniform asymptotics" proposed by Bassom, Clarkson, Law and McLeod [3], we provide a simpler and more rigorous proof of the connection formulas of the Clarkson–McLeod solution for the fourth Painlevé transcendent, which has been established earlier by Its and Kapaev [11] via the isomonodromy and Riemann–Hilbert methods.
Purely functional lazy non-deterministic programming
Authors: Fischer Sebastian , Kiselyov Oleg , Shan Chung-chieh
Published: October 2009

Functional logic programming and probabilistic programming have demonstrated the broad benefits of combining laziness (non-strict evaluation with sharing of the results) with non-determinism. Yet these benefits are seldom enjoyed in functional programming, because the existing features for non-strictness, sharing, and non-determinism in functional languages are tricky to combine.

We present a practical way to write purely functional lazy non-deterministic programs that are efficient and perspicuous. We achieve this goal by embedding the programs into existing languages (such as Haskell, SML, and OCaml) with high-quality implementations, by making choices lazily and representing data with non-deterministic components, by working with custom monadic data types and search strategies, and by providing equational laws for the programmer to reason about their code.
Safe functional reactive programming through dependent types
Authors: Sculthorpe Neil , Nilsson Henrik
Published: October 2009

Functional Reactive Programming (FRP) is an approach to reactive programming where systems are structured as networks of functions operating on signals. FRP is based on the synchronous data-flow paradigm and supports both continuous-time and discrete-time signals (hybrid systems). What sets FRP apart from most other languages for similar applications is its support for systems with dynamic structure and for higher-order reactive constructs.

Statically guaranteeing correctness properties of programs is an attractive proposition. This is true in particular for typical application domains for reactive programming such as embedded systems. To that end, many existing reactive languages have type systems or other static checks that guarantee domain-specific properties, such as feedback loops always being well-formed. However, they are limited in their capabilities to support dynamism and higher-order data-flow compared with FRP. Thus, the onus of ensuring such properties of FRP programs has so far been on the programmer as established static techniques do not suffice.

In this paper, we show how dependent types allow this concern to be addressed. We present an implementation of FRP embedded in the dependently-typed language Agda, leveraging the type system of the host language to craft a domain-specific (dependent) type system for FRP. The implementation constitutes a discrete, operational semantics of FRP, and as it passes the Agda type, coverage, and termination checks, we know the operational semantics is total, which means our type system is safe.
Effective interactive proofs for higher-order imperative programs
Authors: Chlipala Adam , Malecha Gregory , Morrisett Greg , Shinnar Avraham , Wisnesky Ryan
Published: October 2009

We present a new approach for constructing and verifying higher-order, imperative programs using the Coq proof assistant. We build on the past work on the Ynot system, which is based on Hoare Type Theory. That original system was a proof of concept, where every program verification was accomplished via laborious manual proofs, with much code devoted to uninteresting low-level details. In this paper, we present a re-implementation of Ynot which makes it possible to implement fully-verified, higher-order imperative programs with reasonable proof burden. At the same time, our new system is implemented entirely in Coq source files, showcasing the versatility of that proof assistant as a platform for research on language design and verification. Both versions of the system have been evaluated with case studies in the verification of imperative data structures, such as hash tables with higher-order iterators. The verification burden in our new system is reduced by at least an order of magnitude compared to the old system, by replacing manual proof with automation. The core of the automation is a simplification procedure for implications in higher-order separation logic, with hooks that allow programmers to add domain-specific simplification rules.

We argue for the effectiveness of our infrastructure by verifying a number of data structures and a packrat parser, and we compare to similar efforts within other projects. Compared to competing approaches to data structure verification, our system includes much less code that must be trusted; namely, about a hundred lines of Coq code defining a program logic. All of our theorems and decision procedures have or build machine-checkable correctness proofs from first principles, removing opportunities for tool bugs to create faulty verifications.
Experience report
Authors: Sampson Curt J.
Published: October 2009

I describe the initial attempt of experienced business software developers with minimal functional programming background to write a non-trivial, business-critical application entirely in Haskell. Some parts of the application domain are well suited to a mathematically-oriented language; others are more typically done in languages such as C++.

I discuss the advantages and difficulties of Haskell in these circumstances, with a particular focus on issues that commercial developers find important but that may receive less attention from the academic community.

I conclude that, while academic implementations of "advanced" programming languages arguably may lag somewhat behind implementations of commercial languages in certain ways important to businesses, this appears relatively easy to fix, and that the other advantages that they offer make them a good, albeit long-term, investment for companies where effective IT implementation can offer a crucial advantage to success.
Experience report
Authors: Pagano Bruno , Andrieu Olivier , Moniot Thomas , Canou Benjamin , Chailloux Emmanuel , Wang Philippe , Manoury Pascal , Colaço Jean-Louis
Published: October 2009

High-level tools have become unavoidable in industrial software development processes. Safety-critical embedded programs don't escape this trend. In the context of safety-critical embedded systems, the development processes follow strict guidelines and requirements. The development quality assurance applies as much to the final embedded code, as to the tools themselves. The French company Esterel Technologies decided in 2006 to base its new SCADE SUITE 6TM certifiable code generator on Objective Caml. This paper outlines how it has been challenging in the context of safety critical software development by the rigorous norms DO-178B, IEC 61508, EN 50128 and such.
Does conduit artery diameter vary according to the anthropometric characteristics of children or men?
Authors: Hopkins N. D. , Green D. J. , Tinken T. M. , Sutton L. , McWhannell N. , Thijssen D. H. J. , Cable N. T. , Stratton G. , George K.
Published: October 2009

Arterial measurements are commonly undertaken to assess acute and chronic adaptations to exercise. Despite the widespread adoption of scaling practices in cardiac research, the relevance of scaling for body size and/or composition has not been addressed for arterial measures. We therefore investigated the relationships between brachial artery diameter and body composition in 129 children aged 9 to 10 yr (75 girls and 54 boys), and 50 men aged 16–49 yr. Body composition variables (total, lean, and fat mass in the whole body, arm, and forearm) were assessed by dual-energy X-ray absorptiometry, and brachial artery diameter was measured using high-resolution ultrasound. Bivariate correlations were performed, and arterial diameter was then scaled using simple ratios ( y/ x) and allometric approaches after log-log least squares linear regression and production of allometric exponents ( b) and construction of power function ratios ( y/ x b). Size independence was checked via bivariate correlations ( x: y/ x; x: y/ x b). As a result, significant correlations existed between brachial artery diameter and measures of body mass and lean mass in both cohorts ( r = 0.21–0.48, P < 0.05). There were no significant relationships between diameter and fat mass. All b exponents were significantly different from 1 (0.08–0.50), suggesting that simple ratio scaling approaches were likely to be flawed. This was confirmed when ratio scaling produced negative residual size correlations, whereas allometric scaling produced size-independent indexes ( r = 0.00 to 0.03, P > 0.05). In conclusion, when between- or within-group comparisons are performed under circumstances where it is important to control for differences in body size or composition, allometric scaling of artery diameter should be adopted rather than ratio scaling. Our data also suggest that scaling for lean or total mass may be more appropriate than scaling for indexes of fat mass.
Inhibition of matrix metalloproteinase activity in vivo protects against vascular hyporeactivity in endotoxemia
Authors: Cena Jonathan J. , Lalu Manoj M. , Cho Woo Jung , Chow Ava K. , Bagdan Mariel L. , Daniel Edwin E. , Castro Michele M. , Schulz Richard
Published: October 2009

Persistent arterial hypotension is a hallmark of sepsis and is believed to be caused, at least in part, by excess nitric oxide (NO). NO can combine with superoxide to produce peroxynitrite, which activates matrix metalloproteinases (MMPs). Whether MMP inhibition in vivo protects against vascular hyporeactivity induced by endotoxemia is unknown. Male Sprague-Dawley rats were administered either bacterial lipopolysaccharide (LPS, 4 mg/kg ip) or vehicle (pyrogen-free water). Later (30 min), animals received the MMP inhibitor doxycycline (4 mg/kg ip) or vehicle (pyrogen-free water). After LPS injection (6 h), animals were killed, and aortas were excised. Aortic rings were mounted in organ baths, and contractile responses to phenylephrine or KCl were measured. Aortas and plasma were examined for MMP activity by gelatin zymography. Aortic MMP and inducible nitric oxide synthase (iNOS) were examined by immunoblot and/or immunohistochemistry. Doxycycline prevented the LPS-induced development of ex vivo vascular hyporeactivity to phenylephrine and KCl. iNOS protein was significantly upregulated in aortic homogenates from endotoxemic rats; doxycycline did not alter its level. MMP-9 activity was undetectable in aortic homogenates from LPS-treated rats but significantly upregulated in the plasma; this was attenuated by doxycycline. Plasma MMP-2 activities were unchanged by LPS. Specific MMP-2 activity was increased in aortas from LPS-treated rats. This study demonstrates the in vivo protective effect of the MMP inhibitor doxycycline against the development of vascular hyporeactivity in endotoxemic rats.
Caspase-mediated protein kinase C-δ cleavage is necessary for apoptosis of vascular smooth muscle cells
Authors: Kato Kaori , Yamanouchi Dai , Esbona Karla , Kamiya Kentaro , Zhang Fan , Kent K. Craig , Liu Bo
Published: October 2009

Apoptotic death of vascular smooth muscle cells (SMCs) is a prominent feature of blood vessel remodeling and various vascular diseases. We have previously shown that protein kinase C-δ (PKC-δ) plays a critical role in SMC apoptosis. In this study, we tested the importance of PKC-δ proteolytic cleavage and tyrosine phosphorylation within the apoptosis pathway. Using hydrogen peroxide as a paradigm for oxidative stress, we showed that proteolytic cleavage of PKC-δ occurred in SMCs that underwent apoptosis, while tyrosine phosphorylation was detected only in necrotic cells. Furthermore, using a peptide (z-DIPD-fmk) that mimics the caspase-3 binding motif within the linker region of PKC-δ, we were able to prevent the cleavage of PKC-δ, as well as apoptosis. Inhibition of PKC-δ with rottlerin or small-interfering RNA diminished caspase-3 cleavage, caspase-3 activity, cleavage of poly (ADP-ribose) polymerase, cleavage of PKC-δ, and DNA fragmentation, confirming the previously reported role of PKC-δ in initiation of apoptosis. In contrast, z-DIPD-fmk markedly diminished caspase-3 activity, cleavage of PKC-δ, and DNA fragmentation without affecting cleavage of caspase-3 and poly (ADP-ribose) polymerase. Taken together, our data suggest that caspase-3-mediated PKC-δ cleavage underlies SMC apoptosis induced by oxidative stress, and that PKC-δ acts both upstream and downstream of caspase-3.
Direct evidence of a role for Nox2 in superoxide production, reduced nitric oxide bioavailability, and early atherosclerotic plaque formation in ApoE−/−mice
Authors: Judkins Courtney P. , Diep Henry , Broughton Brad R. S. , Mast Anja E. , Hooker Elizabeth U. , Miller Alyson A. , Selemidis Stavros , Dusting Gregory J. , Sobey Christopher G. , Drummond Grant R.
Published: October 2009

The Nox family NADPH oxidases are reactive oxygen species (ROS)-generating enzymes that are strongly implicated in atherogenesis. However, no studies have examined which Nox isoform(s) are involved. Here we investigated the role of the Nox2-containing NADPH oxidase in atherogenesis in apolipoprotein E-null (ApoE−/−) mice. Wild-type (C57Bl6/J), ApoE−/−, and Nox2−/y/ApoE−/−mice were maintained on a high-fat (21%) diet from 5 wk of age until they were 12 or 19 wk old. Mice were euthanized and their aortas removed for measurement of Nox2 expression (Western blot analysis and immunohistochemistry), ROS production (L012-enhanced chemiluminescence), nitric oxide (NO) bioavailability (contractions to Nω-nitro-l-arginine), and atherosclerotic plaque development along the aorta and in the aortic sinus. Nox2 expression was upregulated in the aortic endothelium of ApoE−/−mice before the appearance of lesions, and this was associated with elevated ROS levels. Within developing plaques, macrophages were also a prominent source of Nox2. The absence of Nox2 in Nox2−/y/ApoE−/−double-knockout mice had minimal effects on plasma lipids or lesion development in the aortic sinus in animals up to 19 wk of age. However, an en face examination of the aorta from the arch to the iliac bifurcation revealed a 50% reduction in lesion area in Nox2−/y/ApoE−/−versus ApoE−/−mice, and this was associated with a marked decrease in aortic ROS production and an increased NO bioavailability. In conclusion, this is the first demonstration of a role for Nox2-NADPH oxidase in vascular ROS production, reduced NO bioavailability, and early lesion development in ApoE−/−mice, highlighting this Nox isoform as a potential target for future therapies for atherosclerosis.
Differential expression of platelet-activating factor acetylhydrolase in lung macrophages
Authors: Howard Katherine M.
Published: October 2009

Platelet-activating factor (PAF) acetylhydrolase plays a crucial role inactivating the potent inflammatory mediator, PAF. PAF is implicated in the initiation and propagation of acute lung injury. Although PAF acetylhydrolase is a constitutively active plasma protein, increased PAF production during inflammatory events may necessitate an increase in PAF acetylhydrolase activity in the local environment. A series of experiments were conducted to determine whether the systemic administration of LPS to Sprague-Dawley rats resulted in enhanced expression of PAF acetylhydrolase in lung tissue. Ribonuclease protection assays revealed a dramatic increase in PAF acetylhydrolase mRNA, which peaked at 24 h following in vivo LPS administration. The increase in PAF acetylhydrolase mRNA was dose dependent and was detected when as little as 10 μg/kg of LPS was administered. Western blot analyses of lung tissue homogenates confirmed an increased production of PAF acetylhydrolase protein in response to LPS. In addition, Western blot analyses revealed the rat PAF acetylhydrolase protein exhibited heterogeneous molecular weights with predominant species migrating at 63 and 67 kDa. Some of the molecular weight heterogeneity likely resulted from extensive glycosylation of the secreted protein. Immunohistochemical analyses of lung tissue sections and colocalization experiments revealed a heterogenous population of cells that express the plasma-type PAF acetylhydrolase. Lung interstitial macrophages were PAF acetylhydrolase positive, but surprisingly, alveolar macrophages did not increase expression of PAF acetylhydrolase in response to systemic LPS administration. In addition, rat granulocytes consisting primarily of neutrophils were strongly positive for PAF acetylhydrolase in the LPS-exposed lung tissue. The absence of immunoreactive PAF acetylhydrolase in alveolar macrophages obtained from bronchial alveolar lavage confirmed that systemic LPS administration resulted in enhanced PAF acetylhydrolase expression only in a subset of lung macrophages.
Inhaled nitric oxide improves lung structure and pulmonary hypertension in a model of bleomycin-induced bronchopulmonary dysplasia in neonatal rats
Authors: Tourneux Pierre , Markham Neil , Seedorf Gregory , Balasubramaniam Vivek , Abman Steven H.
Published: October 2009

Whether inhaled nitric oxide (iNO) prevents the development of bronchopulmonary dysplasia (BPD) in premature infants is controversial. In adult rats, bleomycin (Bleo) induces lung fibrosis and pulmonary hypertension, but the effects of Bleo on the developing lung and iNO treatment on Bleo-induced neonatal lung injury are uncertain. Therefore, we sought to determine whether early and prolonged iNO therapy attenuates changes of pulmonary vascular and alveolar structure in a model of BPD induced by Bleo treatment of neonatal rats. Sprague-Dawley rat pups were treated with Bleo (1 mg/kg ip daily) or vehicle (controls) from day 2 to 10, followed by recovery from day 11 to 19. Treatment groups received early ( days 2–10), late ( days 11–19), or prolonged iNO therapy (10 ppm; days 2–19). We found that compared with controls, Bleo increased right ventricular hypertrophy (RVH), and pulmonary arterial wall thickness, and reduced vessel density alveolarization. In each iNO treatment group, iNO decreased RVH ( P < 0.01) and wall thickness ( P < 0.01) and restored vessel density after Bleo ( P < 0.05). iNO therapy improved alveolarization for each treatment group after Bleo; however, the values remained abnormal compared with controls. Prolonged iNO treatment had greater effects on lung structure after bleomycin than late treatment alone. We conclude that Bleo induces lung structural changes that mimic BPD in neonatal rats, and that early and prolonged iNO therapy prevents right ventricle hypertrophy and pulmonary vascular remodeling and partially improves lung structure.
Strict Contractive Conditions and Common Fixed Point Theorems in Cone Metric Spaces
Authors: Kadelburg Z. , Radenović S. , Rosić B.
Published: October 2009

A lot of authors have proved various common fixed-point results for pairs of self-mappings under strict contractive conditions in metric spaces. In the case of cone metric spaces, fixed point results are usually proved under assumption that the cone is normal. In the present paper we prove common fixed point results under strict contractive conditions in cone metric spaces using only the assumption that the cone interior is nonempty. We modify the definition of property (E.A), introduced recently in the work by Aamri and Moutawakil (2002), and use it instead of usual assumptions about commutativity or compatibility of the given pair. Examples show that the obtained results are proper extensions of the existing ones.
A Bayesian Abstract Economy with a Measure Space of Agents
Authors: Patriche Monica
Published: October 2009

We define the model of an abstract economy with differential (asymmetric) information and a measure space of agents. We generalize N. C. Yannelis′s result (2007), considering that each agent is characterised by a random preference correspondence instead of having a random utility function. We establish two different equilibrium existence results.