bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimum Sizing of the Prime Mover in a Medium Scale Gas Turbine CHP System
Authors: Meybodi Mehdi Aghaei , Behnia Masud
Published: May 2011

Optimum selection of prime movers in combined heat and power (CHP) systems is of crucial importance due to the fact that inappropriate choices reduce the benefits of CHP systems considerably. In the selection procedure, the performance characteristics of prime movers as well as economic parameters should be taken into account. In this paper, a thermo-economic method for selecting the optimum nominal power and planning the operational strategy of gas turbine as the prime mover of a medium scale (500–5000 kW) CHP system is presented. Appropriate relations for estimating thermodynamic and economic parameters of the system in the context of net annual cost criterion are introduced. Three modes of operation have been considered, namely, two-way connection (TWC) mode, one-way connection (OWC) mode, and heat demand following (HDF) mode. In TWC mode, buying electricity from the grid and selling the excess electricity to the grid are allowed. OWC mode is a situation in which it is only possible to buy electricity from the grid. In HDF mode, buying electricity from the grid and selling electricity to the grid are allowed. HDF mode of operation is considered to have the minimum waste of energy due to the fact that prime movers work in a condition at which the excess produced heat is minimal. As a way of dealing with the environmental concerns, the impact of carbon tax has also been studied. The proposed method has been used for a case study. It was observed that the optimum nominal powers in TWC mode, OWC mode, and HDF mode are 3.5 MW, 3.4 MW, and 0.8 MW, respectively. Furthermore, in order to determine the sensitivity of results to parameters such as cost of electricity, cost of fuel, and carbon tax, a comprehensive sensitivity analysis was conducted. It is noted that the proposed method may be used for other types of prime movers (such as internal combustion engines) as well as various sizes of combined heat and power systems.
Transrepression of Inflammation
Authors: Foley John F.
Published: May 2011

Estrogen receptor β blocks inflammation in a mouse model of multiple sclerosis by transrepressing gene expression.
Ecology and Evolution as Targets: the Need for Novel Eco-Evo Drugs and Strategies To Fight Antibiotic Resistance
Authors: Baquero Fernando , Coque Teresa M. , de la Cruz Fernando
Published: May 2011

In recent years, the explosive spread of antibiotic resistance determinants among pathogenic, commensal, and environmental bacteria has reached a global dimension. Classical measures trying to contain or slow locally the progress of antibiotic resistance in patients on the basis of better antibiotic prescribing policies have clearly become insufficient at the global level. Urgent measures are needed to directly confront the processes influencing antibiotic resistance pollution in the microbiosphere. Recent interdisciplinary research indicates that new eco-evo drugs and strategies, which take ecology and evolution into account, have a promising role in resistance prevention, decontamination, and the eventual restoration of antibiotic susceptibility. This minireview summarizes what is known and what should be further investigated to find drugs and strategies aiming to counteract the “four P's,” penetration, promiscuity, plasticity, and persistence of rapidly spreading bacterial clones, mobile genetic elements, or resistance genes. The term “drug” is used in this eco-evo perspective as a tool to fight resistance that is able to prevent, cure, or decrease potential damage caused by antibiotic resistance, not necessarily only at the individual level (the patient) but also at the ecological and evolutionary levels. This view offers a wealth of research opportunities for science and technology and also represents a large adaptive challenge for regulatory agencies and public health officers. Eco-evo drugs and interventions constitute a new avenue for research that might influence not only antibiotic resistance but the maintenance of a healthy interaction between humans and microbial systems in a rapidly changing biosphere.
Reversible Daptomycin Tolerance of Adherent Staphylococci in an Implant Infection Model
Authors: John Anne-K. , Schmaler Mathias , Khanna Nina , Landmann Regine
Published: May 2011

Daptomycin (DAP) is bactericidal against methicillin-resistant
Staphylococcus aureus
(MRSA)
in vitro
, but it failed to eradicate MRSA in an experimental model of implant-associated infection. We therefore investigated various factors which could explain treatment failure by evaluating DAP activity, including the role of different cell wall components, adherence, biofilm, and calcium ions (Ca
2+
)
in vitro
and
in vivo
. In the tissue cage infection model, DAP was active only prophylactically and against low inocula. To identify the mechanisms of treatment failure, the
in vitro
activity of DAP against planktonic and adherent growing
S. aureus
and
S. epidermidis
mutants, differing in their capacity of biofilm formation and adherence, was determined. For planktonic staphylococci, the MIC was 0.625 μg/ml. For adherent staphylococci, DAP reduced biofilms at 30 μg/ml. However, it did not kill adherent bacteria up to 500 μg/ml, independent of biofilm biosynthesis (the
ica
mutant strain), nuclease (the
nuc1
/
nuc2
mutant strain), LPXTG-anchored adhesin (the
srtA
mutant strain), autolysin (the
atl
mutant strain), or alanyl-LTA (the
dltA
mutant strain). Resistance of adherent staphylococci was not due to mutations of adherent bacteria, since staphylococci became DAP susceptible after detachment. Phenotypic tolerance was not explained by inactivation of DAP or inability of initial Ca
2+
-DAP complex formation. However, the addition of up to 100 mg/liter (2.5 mmol/liter) Ca
2+
gradually improved bactericidal activity toward adherent staphylococci
in vitro
and increased the prevention rate in the cage model from 40% to 60%. In summary, adherent staphylococci are resistant to DAP killing unless Ca
2+
is supplemented to physiologic concentrations.
Antiviral Activity and Mode of Action of TMC647078, a Novel Nucleoside Inhibitor of the Hepatitis C Virus NS5B Polymerase
Authors: Berke Jan Martin , Vijgen Leen , Lachau-Durand Sophie , Powdrill Megan H. , Rawe Svea , Sjuvarsson Elena , Eriksson Staffan , Götte Matthias , Fransen Els , Dehertogh Pascale , Van den Eynde Christel , Leclercq Laurent , Jonckers Tim H. M. , Raboisson Pierre , Nilsson Magnus , Samuelsson Bertil , Rosenquist Åsa , Fanning Gregory C. , Lin Tse-I
Published: May 2011

Chronic infection with hepatitis C virus (HCV) is a major global health burden and is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma. Current therapy for HCV infection has limited efficacy, particularly against genotype 1 virus, and is hampered by a range of adverse effects. Therefore, there is a clear unmet medical need for efficacious and safe direct antiviral drugs for use in combination with current treatments to increase cure rates and shorten treatment times. The broad genotypic coverage achievable with nucleosides or nucleotides and the high genetic barrier to resistance of these compounds observed
in vitro
and
in vivo
suggest that this class of inhibitors could be a valuable component of future therapeutic regimens. Here, we report the
in vitro
inhibitory activity and mode of action of 2′-deoxy-2′-spirocyclopropylcytidine (TMC647078), a novel and potent nucleoside inhibitor of the HCV NS5B RNA-dependent RNA polymerase that causes chain termination of the nascent HCV RNA chain.
In vitro
combination studies with a protease inhibitor resulted in additive efficacy in the suppression of HCV RNA replication, highlighting the potential for the combination of these two classes in the treatment of chronic HCV infection. No cytotoxic effects were observed in various cell lines. Biochemical studies indicated that TMC647078 is phosphorylated mainly by deoxycytidine kinase (dCK) without inhibiting the phosphorylation of the natural substrate, and high levels of triphosphate were observed in Huh7 cells and in primary hepatocytes
in vitro
. TMC647078 is a potent novel nucleoside inhibitor of HCV replication with a promising
in vitro
virology and biology profile.
Antimicrobial Properties of MX-2401, an Expanded-Spectrum Lipopeptide Active in the Presence of Lung Surfactant
Authors: Dugourd Dominique , Yang Haiyan , Elliott Melissa , Siu Raymond , Clement Jacob J. , Straus Suzana K. , Hancock Robert E. W. , Rubinchik Evelina
Published: May 2011

MX-2401 is an expanded-spectrum lipopeptide antibiotic selective for Gram-positive bacteria that is a semisynthetic analog of the naturally occurring lipopeptide amphomycin. It was active against
Enterococcus
spp., including vancomycin-sensitive
Enterococcus
(VSE),
vanA
-,
vanB
-, and
vanC
-positive vancomycin-resistant
Enterococcus
(VRE), linezolid- and quinupristin-dalfopristin-resistant isolates (MIC
90
of 4 μg/ml), methicillin-resistant
Staphylococcus aureus
(MRSA) and methicillin-sensitive
S. aureus
(MSSA) (MIC
90
of 2 μg/ml), coagulase-negative staphylococci, including methicillin-sensitive
Staphylococcus epidermidis
(MSSE) and methicillin-resistant
S. epidermidis
(MRSE) (MIC
90
of 2 μg/ml), and
Streptococcus
spp. including viridans group streptococci, and penicillin-resistant, penicillin-sensitive, penicillin-intermediate and macrolide-resistant isolates of
Streptococcus pneumoniae
(MIC
90
of 2 μg/ml). MX-2401 demonstrated a dose-dependent postantibiotic effect varying from 1.5 to 2.4 h. Furthermore, MX-2401 was rapidly bactericidal at 4 times the MIC against
S. aureus
and
Enterococcus faecalis
, with more than 99.9% reduction in viable bacterial attained at 4 and 24 h, respectively. The MICs of MX-2401 against MRSA, MSSA, VSE, and VRE strains serially exposed for 15 passages to sub- to supra-MICs of MX-2401 remained within three dilutions of the original MIC. In contrast to that of the lipopeptide daptomycin, the antibacterial activity of MX-2401 was not affected
in vitro
by the presence of lung surfactant, and MX-2401 was active
in vivo
in the bronchial-alveolar pneumonia mouse model, in which daptomycin failed to show any activity. Moreover, the activity of MX-2401 was not as strongly dependent on the Ca
2+
concentration as is the activity of daptomycin. In conclusion, MX-2401 is a promising new-generation lipopeptide for the treatment of serious infections with Gram-positive bacteria, including hospital-acquired pneumonia.
Moraxella catarrhalis
Outer Membrane Vesicles Carry β-Lactamase and Promote Survival of
Streptococcus pneumoniae
and
Haemophilus influenzae
by Inactivating Amoxicillin
Authors: Schaar Viveka , Nordström Therése , Mörgelin Matthias , Riesbeck Kristian
Published: May 2011

Moraxella catarrhalis
is a common pathogen found in children with upper respiratory tract infections and in patients with chronic obstructive pulmonary disease during exacerbations. The bacterial species is often isolated together with
Streptococcus pneumoniae
and
Haemophilus influenzae
. Outer membrane vesicles (OMVs) are released by
M. catarrhalis
and contain phospholipids, adhesins, and immunomodulatory compounds such as lipooligosaccharide. We have recently shown that
M. catarrhalis
OMVs exist in patients upon nasopharyngeal colonization. As virtually all
M. catarrhalis
isolates are β-lactamase positive, the goal of this study was to investigate whether
M. catarrhalis
OMVs carry β-lactamase and to analyze if OMV consequently can prevent amoxicillin-induced killing. Recombinant β-lactamase was produced and antibodies were raised in rabbits. Transmission electron microscopy, flow cytometry, and Western blotting verified that OMVs carried β-lactamase. Moreover, enzyme assays revealed that
M. catarrhalis
OMVs contained active β-lactamase. OMVs (25 μg/ml) incubated with amoxicillin for 1 h completely hydrolyzed amoxicillin at concentrations up to 2.5 μg/ml. In functional experiments, preincubation of amoxicillin (10× MIC) with
M. catarrhalis
OMVs fully rescued amoxicillin-susceptible
M. catarrhalis
,
S. pneumoniae
, and type b or nontypeable
H. influenzae
from β-lactam-induced killing. Our results suggest that the presence of amoxicillin-resistant
M. catarrhalis
originating from β-lactamase-containing OMVs may pave the way for respiratory pathogens that by definition are susceptible to β-lactam antibiotics.
New Fks Hot Spot for Acquired Echinocandin Resistance in
Saccharomyces cerevisiae
and Its Contribution to Intrinsic Resistance of
Scedosporium
Species
Authors: Johnson Michael E. , Katiyar Santosh K. , Edlind Thomas D.
Published: May 2011

Echinocandins represent a new antifungal group with potent activity against
Candida
species. These lipopeptides inhibit the synthesis of β-1,3-glucan, the major cell wall polysaccharide. Acquired resistance or reduced echinocandin susceptibility (RES) is rare and associated with mutations in two “hot spot” regions of Fks1 or Fks2, the probable β-1,3-glucan synthases. In contrast, many fungi demonstrate intrinsic RES for reasons that remain unclear. We are using
Saccharomyces cerevisiae
to understand the basis for RES by modeling echinocandin-Fks interaction. Previously characterized mutations confer cross-RES; we screened for mutations conferring differential RES, implying direct interaction of that Fks residue with a variable echinocandin side chain. One mutant (in an
fks1
Δ background) exhibited ≥16-fold micafungin and anidulafungin versus caspofungin RES. Sequencing identified a novel Fks2 mutation, W714L/Y715N. Equivalent W695L/Y696N and related W695L/F/C mutations in Fks1 generated by site-directed mutagenesis and the isolation of a W695L-equivalent mutation in
Candida glabrata
confirmed the role of the new “hot spot 3” in RES. Further mutagenesis expanded hot spot 3 to Fks1 residues 690 to 700, yielding phenotypes ranging from cross-RES to differential hypersusceptibility. Fks1 sequences from intrinsically RES
Scedosporium
species revealed W695F-equivalent substitutions; Fks1 hybrids expressing
Scedosporium prolificans
hot spot 3 confirmed that this substitution imparts RES.
Requirement for Invariant Chain in Macrophages for Mycobacterium tuberculosis Replication and CD1d Antigen Presentation
Authors: Sillé Fenna C. M. , Martin Constance , Jayaraman Pushpa , Rothchild Alissa , Fortune Sarah , Besra Gurdyal S. , Behar Samuel M. , Boes Marianne
Published: May 2011

Mycobacterium tuberculosisis an intracellular bacterium that persists in phagosomes of myeloid cells.M. tuberculosis-encoded factors support pathogen survival and reduce fusion of phagosomes with bactericidal lysosomal compartments. It is, however, not entirely understood if host factors that mediate endosomal fusion affectM. tuberculosisintracellular localization and survival. Neither is it known if endosomal fusion influences induction of host immune reactivity byM. tuberculosis-infected cells. Lysosomal degradation ofM. tuberculosisappears to be pivotal for making available lipid substrates for assembly into lipid-CD1d complexes to allow activation of CD1d-restricted invariant natural killer T (iNKT) cells. To clarify the role for endosomal fusion inM. tuberculosissurvival and induction of host CD1d-mediated immune defense, we focused our studies on the invariant chain (Ii). Ii regulates endosome docking and fusion and thereby controls endosomal transport. Through direct binding, Ii also directs intracellular transport of the class II major histocompatibility complex and CD1d. Our findings demonstrate that upon infection of Ii-knockout (Ii−/−) macrophages,M. tuberculosisis initially retained in early endosomal antigen 1-positive lysosomal-associated membrane protein 1-negative phagosomes, which results in slightly impaired pathogen replication. The absence of Ii did not affect the ability of uninfected and infected macrophages to produce nitric oxide, tumor necrosis factor alpha, or interleukin-12. However, induction of cell surface CD1d was impaired in infected Ii−/−macrophages, and CD1d-restricted iNKT cells were unable to suppress bacterial replication when they were cocultured withM. tuberculosis-infected Ii−/−macrophages. Thus, while the host factor Ii is not essential for the formation of theM. tuberculosis-containing vacuole, its presence is crucial for iNKT cell recognition of infected macrophages.
Attenuated Nephritis in Inducible Nitric Oxide Synthase Knockout C57BL/6 Mice and Pulmonary Hemorrhage in CB17 SCID and Recombination Activating Gene 1 Knockout C57BL/6 Mice Infected with Leptospira interrogans
Authors: Bandeira Maurício , Santos Cleiton S. , de Azevedo Everton C. , Soares Luciane Marieta , Macedo Júlio O. , Marchi Samyra , da Silva Caroline Luane R. , Chagas-Junior Adenizar D. , McBride Alan J. A. , McBride Flávia W. C. , Reis Mitermayer G. , Athanazio Daniel A.
Published: May 2011

The aims of this study were to investigate the frequency of pulmonary hemorrhage (PH) in mice unable to produce functional B and T lymphocytes and to explore the effect of an inducible nitric oxide synthase gene (
Inos
) knockout (KO) on the frequency/severity of interstitial nephritis
in vivo
. We studied the outcome of infection by the virulent
Leptospira interrogans
serovar Copenhageni strain Cop. The animals used were
Inos
KO mice, recombination activating gene 1 (
Rag1
) KO mice, CB17 severe combined immunodeficiency (SCID) mice, and the respective wild-type (WT) C57BL/6 and BALB/c controls. The
Inos
KO and WT mice survived with no clinical symptoms of leptospirosis. The frequency and severity of nephritis was significantly lower in the
Inos
KO mice. All of the
Rag1
KO and SCID animals died of acute leptospirosis, whereas all of the WT mice survived. PH was observed in 57 and 94% of
Rag1
KO mice and in 83 and 100% of SCID mice, using inoculum doses of 10
7
and 10
6
leptospires, respectively. There was no evidence of PH in the WT controls. In conclusion, the loss of the
Inos
gene had a negligible effect on the outcome of leptospiral infection, although we observed a reduced susceptibility for interstitial nephritis in this group. Of note, the absence of functional B- and T-cell lymphocytes did not preclude the occurrence of PH. These data provide evidence that PH in leptospirosis may not be related only to autoimmune mechanisms.
Expression of the Type 1 Pneumococcal Pilus Is Bistable and Negatively Regulated by the Structural Component RrgA
Authors: Basset Alan , Turner Keith H. , Boush Elizabeth , Sayeed Sabina , Dove Simon L. , Malley Richard
Published: May 2011

The pneumococcal type 1 pilus, which is present in 25 to 30% of clinical isolates, has been associated with increased adherence and inflammatory responses and is being evaluated as a potential vaccine candidate. Here we show that expression of the pilus is bistable as a result of the molecular interaction between the transcription activator RrlA and a structural component of the pilus called RrgA. Sampling various clinical pneumococcal isolates that harbor the type 1 pilus-encoding islet, we show that distinct populations of cells can be identified with either undetectable or prominent pilus expression. When these two populations are separated and regrown in liquid medium, they are phenotypically different: the nonexpressing population reverts to the previous bimodal distribution, whereas the expressing population retains the same high level of pilus expression. Controlled exogenous expression of the regulatory pilus gene
rlrA
in a strain from which the endogenous version has been deleted increases pilus expression steadily, suggesting that the bistable expression of the pilus observed in wild-type cells is dependent on the native
rlrA
promoter. Finally, we demonstrate that RrgA is a negative regulator of pilus expression and that this repression is likely mediated through direct interaction with RlrA. We conclude that type 1 pilus expression in pneumococcus exhibits a bistable phenotype, which is dependent upon the molecular interplay between the RlrA and RrgA proteins. We suggest that this flexibility in expression may assist adaptation to a range of immune conditions, such as evasion of antipilus antibodies, within potential hosts.
A Novel Zinc Binding System, ZevAB, Is Critical for Survival of Nontypeable Haemophilus influenzae in a Murine Lung Infection Model
Authors: Rosadini Charles V. , Gawronski Jeffrey D. , Raimunda Daniel , Argüello José M. , Akerley Brian J.
Published: May 2011

Nontypeable
Haemophilus influenzae
(NTHI) is a Gram-negative bacterial pathogen that causes upper and lower respiratory infections. Factors required for pulmonary infection by NTHI are not well understood. Previously, using high-throughput insertion tracking by deep sequencing (HITS), putative lung colonization factors were identified. Also, previous research indicates that secreted disulfide-dependent factors are important for virulence of
H. influenzae
. In the present study, HITS data were compared with an informatics-based list of putative substrates of the periplasmic oxidoreductase DsbA to find and characterize secreted virulence factors. This analysis resulted in identification of the “
z
inc binding
e
ssential for
v
irulence” (
zev
) locus consisting of
zevA
(HI1249) and
zevB
(HI1248). NTHI mutants of
zevA
and
zevB
grew normally in rich medium but were defective for colonization in a mouse lung model. Mutants also exhibited severe growth defects in medium containing EDTA and were rescued by supplementation with zinc. Additionally, purified recombinant ZevA was found to bind to zinc with high affinity. Together, these data demonstrate that
zevAB
is a novel virulence factor important for zinc utilization of
H. influenzae
under conditions where zinc is limiting. Furthermore, evidence presented here suggests that zinc limitation is likely an important mechanism for host defense against pathogens during lung infection.
Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map
Authors: Reddy Umesh K. , Rong Jun-kang , Nimmakayala Padma , Vajja Gopinath , Rahman Mohammad A , Yu John , Soliman Khairy M. , Heller-Uszynska Katarzyna , Kilian Andrzej , Paterson Andrew H.
Published: May 2011

A diversity array technology (DArT) marker platform was developed for the cotton genome, to evaluate the use of DArT markers compared with AFLP markers in mapping and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium L. that already contained ∼5000 loci, which coalesced into 26 chromosomes, to anchor newly developed DArT and AFLP markers with the aim of further improving utility and map resolution. Our results indicated that the percentage of polymorphic DArT markers that could be genetically mapped (78.15%) was much higher than that of AFLP markers (22.28%). Sequence analysis of DArT markers indicated that a majority matched known expressed sequence tag (EST) sequences from tetraploid and diploid Gossypium species. A total of 794 Arabidopsis genes were homologous with various DArT marker sequences. Chromosomes 5(A), 7(A), 19(D), 23(D), and 24(D) had more Arabidopsis syntenic DArT markers than the other chromosomes. Anchoring DArT markers from the reference map to a recombinant inbred line (RIL) map indicated that DArT markers will speed the building of maps in de novo RIL populations.
GnomCmp: a quantitative approach for comparative analysis of closely related genomes of bacterial pathogens
Authors: Yu GongXin
Published: May 2011

Comparative genome analysis is a powerful approach to understanding the biology of infectious bacterial pathogens. In this study, a quantitative approach, referred to as GnomCmp, was developed to study the microevolution of bacterial pathogens. Although much more time-consuming than existing tools, this procedure provides a much higher resolution. GnomCmpaccomplishes this by establishing genome-wide heterogeneity genotypes, which are then quantified and comparatively analyzed. The heterogeneity genotypes are defined as chromosomal base positions that have multiple variants within particular genomes, resulted from DNA duplications and subsequent mutations. To prove the concept, the procedure was applied on the genomes of 15 Staphylococcus aureus strains, focusing extensively on two pairs of hVISA/VISA strains. hVISA refers to heteroresistant vancomycin-intermediate S. aureus strains and VISA is their VISA mutants. hVISA/VISA displays some remarkable properties. hVISA is susceptible to vancomycin, but VISA mutants emerge soon after a short period of vancomycin therapy, therefore making the pathogen a great model organism for fast-evolving bacterial pathogens. The analysis indicated that GnomCmpcould reveal variants within the genomes, which can be analyzed within the global genome context. GnomCmpdiscovered evolutionary hotspots and their dynamics among many closely related, even isogenic genomes. The analysis thus allows the exploration of the molecular mechanisms behind hVISA/VISA evolution, providing a working hypotheses for experimental testing and validation.
Mitochondrial genome sequences of representatives of three families of scorpionflies (Order Mecoptera) and evolution in a major duplication of coding sequence
Authors: Beckenbach Andrew T
Published: May 2011

The complete mitochondrial DNA sequences of a hangingfly, Bittacus pilicornis (Mecoptera: Bittacidae), a snow scorpion fly, Boreus elegans (Mecoptera: Boreidae), and a nearly complete sequence from another scorpionfly species, Microchorista philpotti (Mecoptera: Nannochoristidae) were determined. The coding sequence of all three genomes includes the 37 genes normally found in insect mtDNAs, in the same gene order as first described in Drosophila. In addition to the standard set of genes, the Microchorista sequence includes a large duplication of the coding region. The duplication is at least 4 kb (and may be much larger) and includes the remnants of three protein-coding genes and seven tRNA genes. The duplication evidently arose as a single event, and the duplicated region can be aligned in its entirety with the corresponding region of the functional genome. Although most of the genes contain defects that render them nonfunctional, analysis shows that the protein-coding genes in the duplicated region evolved for a considerable period under constraints expected of functional protein-coding genes. It is evident, therefore, that for a period two copies of some of the mitochondrial genes were functional in this species, including genes coding for proteins.
Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan, and Europe as determined by nucleotide-binding-site profiling
Authors: Sayar-Turet Muge , Dreisigacker Susanne , Braun Hans-J. , Hede Arne , MacCormack Ruth , Boyd Lesley A.
Published: May 2011

The genetic diversity within wheat breeding programs across Turkey and Kazakhstan was compared with a selection of European cultivars that represented the genetic diversity across eight European countries and six decades of wheat breeding. To focus the measure of genetic diversity on that relevant to disease-resistant phenotypes, nucleotide-binding-site (NBS) profiling was used to detect polymorphisms associated with the NBS motifs found within the NBS – leucine-rich repeat (LRR) class of resistance (R) genes. Cereal-specific NBS primers, designed specifically to the conserved NBS motifs found within cereal R-genes, provided distinct NBS profiles. Although the genetic diversity associated with NBS motifs was only slightly higher within the Eastern wheat genotypes, the NBS profiles produced by Eastern and European wheat lines differed considerably. Structure analysis divided the wheat genotypes into four groups, which compared well with the origin of the wheat genotypes. The highest levels of genetic diversity were seen for the wheat genotypes from the Genetic Resource Collection held in Ankara, Turkey, as wheat genotypes within breeding programs were genetically more similar. The wheat genotypes from Kazakhstan were the most similar to the European cultivars, reflecting the significant number of eastern European cultivars used in the breeding program in Kazakhstan. In general, the NBS profiles suggested that NBS–LRR R-gene usage in winter wheat breeding in Turkey and Kazakhstan differed from that deployed in European cultivars.
Silica-supported barium chloride (SiO2–BaCl2) — Efficient and heterogeneous catalyst for the environmentally friendly preparation of N,N′-alkylidene bisamides under solvent-free conditions
Authors: Mohammad Shafiee Mohammad Reza
Published: May 2011

A series of N,N′-alkylidene bisamides were prepared via a green and environmentally friendly synthetic protocol from the reaction of phenyl acetylene or hex-1-yne, aromatic aldehyde, and benzamide or acetamide. Silica-supported barium chloride (SiO2–BaCl2) catalyzes the process of the reaction. The prepared catalysts were characterized by X-ray diffraction, and the products were obtained with high conversions and yields.
Biaryl crosslinkers. I. Crosslinking of a bisazidobiaryl with poly(3-hexylthiophene)
Authors: Lohani Jaya , Balakrishnan V.R. , Gaur Manoj , Raghunathan P. , Eswaran S.V.
Published: May 2011

A new biaryl-based bisazide has been used to crosslink poly(3-hexylthiophene), a conducting polymer useful for organic electronics. Crosslinking was monitored using infrared spectroscopy and film morphology was studied using scanning electron microscopy. Hole mobility studies of the devices prepared from pristine and crosslinked polymer show an increase in hole mobility of one order of magnitude for the latter devices.
Functionalizing poly(cyclic olefins) using copper-catalyzed azide–alkyne “click” reactions
Authors: Faragher Robert J. , McKay Craig S. , Hoa Xuyen D. , Prikrylova Barbara , Lopinski Gregory P. , Figeys Daniel , Veres Teodor , Pezacki John P.
Published: May 2011

A robust method for functionalizing poly(cyclic olefin) surfaces comprised of Zeonor 1060R was developed. These surfaces were first oxidized using two separate methods, ozonolysis and oxygen plasma treatment, to increase their hydrophilic properties and produce carboxylic acids on the surface. The resulting acids enabled direct amide coupling with various amines containing azide or alkyne moieties onto the surface. These modified surfaces were further functionalized via copper-catalyzed azide–alkyne cycloadditions (CuAAC) on the surface and the method was optimized for this material. Surface modifications were characterized by water contact angle measurements, fluorescence microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Our data demonstrates a robust method for generating “clickable” Zeonor 1060R surfaces as demonstrated through attachment and subsequent detection of a triazole-linked fluorophore. The method developed enables the systematic modification of any poly(cyclic olefin) surface for functionalization using the click reaction.
Partition coefficients of disparlure at hydrophobic/aqueous interfaces: A comparative experimental and theoretical study
Authors: Reimer Sarah , Van Klei Christa , Yu Yang , Plettner Erika , Weinberg Noham
Published: May 2011

The gypsy moth, Lymantria dispar, uses pheromones, such as (+)-disparlure, for communication. These pheromones are detected by the sensitive antennae of the male moth and travel through their aqueous environment to the sensory neuron, possibly with assistance from pheromone binding proteins (PBPs). The hydrophobicity of disparlure, which is of primary importance for its interactions with PBPs, can be measured by its partition coefficients. These coefficients for heptane/water and chloroform/water interfaces were obtained in this work experimentally and using molecular dynamics (MD) simulations. The agreement between the experimental and calculated values validates the choice of the force field parameters, which can thus be used in future MD simulations of the PBP–pheromone interactions.
ALGEBRAIC FOLIATIONS DEFINED BY QUASI-LINES
Authors: BONAVERO LAURENT , HÖRING ANDREAS
Published: May 2011

Let X be a projective manifold containing a quasi-line l. An important difference between quasi-lines and lines in the projective space is that in general there is more than one quasi-line passing through two given general points. In this paper, we use this feature to construct an algebraic foliation associated to a family of quasi-lines. We prove that if the singular locus of this foliation is not too large, it induces a rational fibration on X that maps the general leaf of the foliation onto a quasi-line in a rational variety.
CENTRAL LIMIT THEOREM FOR DIMENSION OF GIBBS MEASURES IN HYPERBOLIC DYNAMICS
Authors: LEPLAIDEUR RENAUD , SAUSSOL BENOÎT
Published: May 2011

For an equilibrium measure of a Hölder potential, we prove an analogue of the Central Limit Theorem for the fluctuations of the logarithm of the measure of balls as the radius goes to zero.

A noticeable consequence is that when this measure is not absolutely continuous, the probability that a ball of radius ε chosen at random have a measure smaller (or larger) than εδ is asymptotically equal to 1/2, where δ is the Hausdorff dimension of the measure.

Our method applies to a class of non-conformal expanding maps on the d-dimensional torus. It also applies to conformal repellers and Axiom A surface diffeomorphisms and possibly to a class of one-dimensional non-uniformly expanding maps. These generalizations are presented at the end of the paper.
Alternating automata on data trees and XPath satisfiability
Authors: Jurdziński Marcin , Lazić Ranko
Published: May 2011

A data tree is an unranked ordered tree whose every node is labeled by a letter from a finite alphabet and an element (“datum”) from an infinite set, where the latter can only be compared for equality. The article considers alternating automata on data trees that can move downward and rightward, and have one register for storing data. The main results are that nonemptiness over finite data trees is decidable but not primitive recursive, and that nonemptiness of safety automata is decidable but not elementary. The proofs use nondeterministic tree automata with faulty counters. Allowing upward moves, leftward moves, or two registers, each causes undecidability. As corollaries, decidability is obtained for two data-sensitive fragments of the XPath query language.
Application-Tailored I/O with Streamline
Authors: de Bruijn Willem , Bos Herbert , Bal Henri
Published: May 2011

Streamline is a stream-based OS communication subsystem that spans from peripheral hardware to userspace processes. It improves performance of I/O-bound applications (such as webservers and streaming media applications) by constructing tailor-made I/O paths through the operating system for each application at runtime. Path optimization removes unnecessary copying, context switching and cache replacement and integrates specialized hardware. Streamline automates optimization and only presents users a clear, concise job control language based on Unix pipelines. For backward compatibility Streamline also presents well known files, pipes and sockets abstractions. Observed throughput improvement over Linux 2.6.24 for networking applications is up to 30-fold, but two-fold is more typical.
Information systems in distributed environments
Authors: Mishra Alok , Münch Jürgen , Mishra Deepti
Published: May 2011

This is a report from a one-day second international workshop on "Information Systems in Distributed Environments" (ISDE), which was organized in conjunction with the OnTheMove Federated Conferences & Workshops (OTM 2010) at Hersonissos-Crete, Greece, on October 26, 2010. The main focus of this workshop was to provide a venue for the discussion of challenges related to the development, operation, and maintenance of distributed information systems, and their creation in the context of global development projects. Further dissemination of research results will lead to an improvement of distributed information system development and deployment across the glob.
Availability state transition model
Authors: Chandra Shalini , Khan Raees Ahmad
Published: May 2011

Several security mechanisms such as digital signature, timestamp audits and trails, encryption, throttling, filtering, protect secrets etc. are available. These security mechanisms are not completely able to stop malicious attacks. For malicious hackers and attackers it is comparatively easy to exploit security loopholes at the user's end side. Behind such type of problem the main reason is bad software design and its implementation without proper risk analysis and mitigation. So, an idea to model availability states an Availability State Transition Model (ASTM) has been proposed in this article. In ASTM methodology, only design level details is required which can be easily retrieved from the software's design.
Testing software fault tolerance techniques
Authors: Choudhary R. K. , Khan R. A.
Published: May 2011

Software fault tolerance can itself be dangerous error-prone because of the additional effort that must be included in the programming process. The paper is based upon research in the area of testing software fault tolerance techniques. A Framework to Test Fault Tolerance has been proposed and validated with industry data. During the validation process we identified some of the interesting findings that can be explored to carry out further research in this area.
Agile management and development of software projects based on collaborative environments
Authors: Franky María Consuelo
Published: May 2011

We've heard of Agile methodologies for several years, but software projects have still delays and failures in planning and management. How then automate the processes of the development of software projects following agile methodologies?

In this paper we try to answer this question by proposing an appropriate use of collaborative environments for software development that effectively translated into action the principles and practices of Agile methodologies. The appropriate use of these collaborative environments leads to a truly agile management, where the project manager achieves the vision and the continuous monitoring of the project, and the participants become adapted to an agile and productive discipline imposed by the environment, regardless if they are geographically dispersed. To ensure that appropriate use, this paper proposes a methodological guide to achieve an agile management of software projects by relying on a particular collaborative environment.
Estimation of generic reusability for object-oriented software an empirical approach
Authors: Gandhi Parul , Bhatia Pradeep Kumar
Published: May 2011

Inheritance and templates are key concepts in object-oriented programming (OOP), and are essential for achieving reusability and extendibility. The aim of this paper is to explore traditional Halstead's metrics and use them to propose more software metrics related to generic method and attributes in an object-oriented software. These metrics measure quantitative generic construct with inheritance in an object-oriented code. Two metrics GRr (Generic Reusability Ratio) and ERr (Effort Ratio) are proposed in this paper. First metric GRr (Generic Reusability Ratio) measures impact of template in program volume and second metric ERr (Effort Ratio) measures impact of template in development effort. These metrics will be a tool for estimating and evaluating costs of program design and program tests as well as program complexity.
Framework for hybrid performance prediction process model
Authors: Geetha D. Evangelin , Kumar T.V. Suresh , Kanth K. Rajani
Published: May 2011

The dynamic behavior of distributed systems requires that their performance characteristics be determined rigorously, preferably in the early stages of software engineering process. Evaluation of the performance at the end of software development leads to increase in the cost of design change. To compare design alternatives or to identify system bottlenecks, quantitative system analysis must be carried out from the early stages of the software development life cycle. In this paper we describe a process model, Hybrid Performance Prediction Process Model that allows modeling and evaluating distributed systems with the explicit goal of assessing performance of the software system during feasibility study. The use case performance engineering approach proposed in this paper exploits use case model and provides flexibility to integrate the software performance prediction process with software engineering process. We use an e-parking application to demonstrate various elements in our framework. The performance metrics are obtained and analyzed by considering two software architectures. Sensitivity analysis on the behavior of resources is carried out. This analysis helps to determine the capacity of the execution environment to obtain the defined performance objectives.
A curriculum for agile software development methodologies
Authors: Mishra Alok , Mishra Deepti
Published: May 2011

Agile software development methodologies are proliferating in software development organizations. Agile techniques can handle changing business requirements, schedule, cost, personnel turnover in an effective way in organizations. Here, major components of agile software development curriculum are discussed along with suggestions towards making it a successful course of software engineering curriculum.
An interview with Bob Metcalfe
Authors: Press Gil
Published: May 2011

Bob Metcalfe thinks we are in a bubble, an innovation bubble, seeing that the word "innovation" is on everybody's lips. To help ensure that this bubble does not burst, he has embarked on a new career path as Professor of Innovation and Murchison Fellow of Free Enterprise at the University of Texas at Austin. This is his fifth career, building on his work as an engineer-scientist leading the invention of Ethernet in the 1970s, entrepreneur-executive and founder of 3Com in the 1980s, publisher-pundit and CEO of InfoWorld in the 1990s, and venture capitalist in the 2000s. As General Partner with Polaris Venture Partners, he has invested primarily in cleantech and currently serves on the boards of five companies: Ember, Sun Catalyx, 1366 Technologies, Infinite Power, and SiOnyx.
Editor's introduction
Authors: Conitzer Vincent
Published: May 2011

I am very happy to introduce Issue 8.2 of SIGecom Exchanges.

The first four contributions concern game theory. The first contribution is a full-length paper by Demaine, Hajiaghayi, Mahini, and Zadimoghaddam, titled "The Price of Anarchy in Cooperative Network Creation Games." In it, they study network creation games, in which the nodes of a graph decide which edges to create. They study "collaborative equilibrium" in which coalitions do not want to change their collective strategy on a single edge, and analyze the price of anarchy in this model. In "Computing Shapley's Saddles," Brandt, Brill, Fischer, Harrenstein, and Hoffmann discuss the computational complexity of saddles, an ordinal, set-valued solution concept defined by Shapley. In "A Prescriptive Approach for Playing Games," Feldman gives an overview of two recent papers on two-player zero-sum games: one of these papers considers a model in which the randomization phase of a randomized strategy is not completely private, and the other considers repeated symmetric games in which one player never observes a single payoff (but does observe the opponent's play). Finally, Pita, Bellamane, Jain, Kiekintveld, Tsai, Ordóñez, and Tambe consider some real-world applications of game theory at Los Angeles International Airport and the US Federal Air Marshals, and discuss some of the challenges in applying game theory to practice, in their letter "Security Applications: Lessons of Real-World Deployment".
Security applications
Authors: Pita James , Bellamane Harish , Jain Manish , Kiekintveld Chris , Tsai Jason , Ordóñez Fernando , Tambe Milind
Published: May 2011

Game theory has played an important role in security decisions. Recent work using Stackelberg games [Fudenberg and Tirole 1991] to model security domains has been particularly influential [Basilico et al. 2009; Kiekintveld et al. 2009; Paruchuri et al. 2008; Pita et al. 2008; Pita et al. 2009]. In a Stackelberg game, a leader (in this case the defender) acts first and commits to a randomized security policy. The follower (attacker) optimizes its reward
considering the strategy chosen by the leader
. These games are well-suited to representing the problem security forces face in allocating limited resources, such as officers, canine units, and checkpoints. In particular, the fact that the attacker is able to observe the policy reflects the way real terrorist organizations plan attacks using extensive surveillance and long planning cycles.
Solution to Exchanges 8.1 puzzle
Authors: Airiau Stéphane , Endriss Ulle , Halpern Joseph Y.
Published: May 2011

The Editor's Puzzle published in SIGeom Exchanges 8.1 was based on an ancient Japanese prophecy [Conitzer 2009]. It was concerned with the complications associated with determining the champion of all warriors. What follows is a synthesis of two correct solutions that were received.
Designing aggregation mechanisms for reputation systems in online marketplaces
Authors: Aperjis Christina , Johari Ramesh
Published: May 2011

A seller in an online marketplace with an effective reputation mechanism should expect that dishonest behavior results in higher payments now, while honest behavior results in higher reputation---and thus higher payments---in the future. We briefly survey recent results on the Window Aggregation Mechanism, a widely used class of mechanisms that shows the average value of the seller's ratings within some fixed window of past transactions. We suggest approaches for choosing the window size that maximizes the range of parameters for which it is optimal for the seller to be truthful. We show that mechanisms that use information from a larger number of past transactions tend to provide incentives for patient sellers to be more truthful, but for higher quality sellers to be less truthful. We then discuss a broader class of aggregation mechanisms that weight recent ratings more heavily and show that the same insight applies.
Competition in mechanisms
Authors: Pai Mallesh M.
Published: May 2011

We consider settings where sellers compete by announcing
auctions
or
mechanisms
. We sketch why, in our opinion, it is important to understand and survey some of the main results to date. We then describe recent results in 2 settings. We conclude with a discussion of directions for future progress.
Approximability of combinatorial problems with multi-agent submodular cost functions
Authors: Goel Gagan , Karande Chinmay , Tripathi Pushkar , Wang Lei
Published: May 2011

Applications in complex systems such as the Internet have spawned a recent interest in studying situations involving multiple agents with their individual cost or utility functions. In this paper, we introduce an algorithmic framework for studying combinatorial optimization problems in the presence of multiple agents with submodular cost functions. We study several fundamental covering problems in this framework and establish upper and lower bounds on their approximability.
An interactive, multi-modal workspace for physically based sound
Authors: Schroeder Benjamin
Published: May 2011

Physically based sound synthesis holds great promise for creating instruments that produce realistic sound but which can go beyond what is possible in the physical world.
Assistive technology commercialization
Authors: Braziller Clay
Published: May 2011

Like many people, I never really considered the Assistive Technology sector a big "Market Opportunity". My views changed quickly after tearing my nearly 50-year-old calf muscle piggy backing a 20 year old. Besides feeling like an old fart I also realized that we are all only temporarily able bodied and that we are all going to need varying degrees of support. In fact, there are now an estimated 30 million people with disabilities in the United States, 21 million of working age. By 2013, these people will purchase $49.3 billion of voice recognition software, eye trackers, sip and puff mice, screen readers, and more. (http://www.bccresearch.com/report/HLC047B.html)