bluuebunny/crossref_metadata_2025 huggingface dataset:
Utilization of cracks to fabricate anodic aluminum oxide nanoporous tubular and rectangular membrane
Authors: Kasi Ajab Khan , Afzulpurkar Nitin , Kasi Jafar Khan , Tuantranont Adisorn , Dulyaseree Paweena
Published: July 2011

The fabrication of nonoporous alumina membrane is a sensitive process. Making small diameter anodic aluminum oxide (AAO) tubular membrane is crucial for applications where large surface area is needed. Hemodialysis, protein separation and molecular sieving are some of target areas where small diameter AAO tubular membrane can be used. In this paper a simple method to fabricate AAO nanoporous tubular and rectangular membrane is introduced. This method is based on cracking behavior of alumina when grown at two faces of aluminum (Al) perpendicular to each other. These cracks are utilized to fabricate 2D and 3D structures such as rectangular and tubular membranes. This method does not need Al tube to fabricate tubular membrane instead a hole is drilled in Al and follow by anodization process. In the anodization process cracks appear at every edge. During Al etching, tubular membrane and plane membrane separates from each other. This method does not need to insulate Al from any side in the electrolyte solution or cutting any surface mechanically. Using this method AAO tubular membranes from 825 μm to 1.8 mm diameter were fabricated successfully. The nanoporous membranes were fabricated from 35 nm up to 81 nm pore diameter and 1.43 μm to 114 μm thickness. The fabricated AAO tubular membranes were uniform and the nanopores were in hexagonal order.
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
Authors: Gladden John M. , Allgaier Martin , Miller Christopher S. , Hazen Terry C. , VanderGheynst Jean S. , Hugenholtz Philip , Simmons Blake A. , Singer Steven W.
Published: July 2011

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli,
Rhodothermus marinus
, and
Thermus thermophilus
. At lower abundance, thermophilic
Chloroflexi
and an uncultivated lineage of the
Gemmatimonadetes
phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
Effect of Soil Clay Content on RNA Isolation and on Detection and Quantification of Bacterial Gene Transcripts in Soil by Quantitative Reverse Transcription-PCR
Authors: Novinscak A. , Filion M.
Published: July 2011

In this study, we evaluated the effect of soil clay content on RNA isolation and on quantitative reverse transcription-PCR (qRT-PCR) quantification of microbial gene transcripts. The amount of clay significantly altered RNA isolation yields and qRT-PCR analyses. Recommendations are made for quantifying microbial gene transcripts in soil samples varying in clay content.
Microbial Utilization and Selectivity of Pectin Fractions with Various Structures
Authors: Onumpai Chatchaya , Kolida Sofia , Bonnin Estelle , Rastall Robert A.
Published: July 2011

To evaluate the fermentation properties of oligosaccharides derived from pectins and their parent polysaccharides, a 5-ml-working-volume, pH- and temperature-controlled fermentor was tested. Six pectic oligosaccharides representing specific substructures found within pectins were prepared. These consisted of oligogalacturonides (average degrees of polymerization [DP] of 5 and 9), methylated oligogalacturonides (average DP of 5), oligorhamnogalacturonides (average DP of 10 as a disaccharide unit of galacturonic acid and rhamnose), oligogalactosides (average DP of 5), and oligoarabinosides (average DP of 6). The influence of these carbohydrates on the human fecal microbiota was evaluated. Use of neutral sugar fractions resulted in an increase inBifidobacteriumpopulations and gave higher organic acid yields. TheBacteroides-Prevotellagroup significantly increased on all oligosaccharides except oligogalacturonides with an average DP of 5. The most selective substrates for bifidobacteria were arabinan, galactan, oligoarabinosides, and oligogalactosides.
Purification and Characterization of the [NiFe]-Hydrogenase of Shewanella oneidensis MR-1
Authors: Shi Liang , Belchik Sara M. , Plymale Andrew E. , Heald Steve , Dohnalkova Alice C. , Sybirna Kateryna , Bottin Hervé , Squier Thomas C. , Zachara John M. , Fredrickson James K.
Published: July 2011

Shewanella oneidensisMR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant withouthyaBandhydAgenes. Expression of recombinant MR-1 [NiFe]-H2ase intransrestored the mutant's ability to produce H2at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2oxidation to reduction of Tc(VII)O4−and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated reduction of Tc(VII)O4−but not methyl viologen. Under the conditions tested, all Tc(VII)O4−used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O4−was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2·nH2O, which was also the product of Tc(VII)O4−reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H2ase catalyzes Tc(VII)O4−reduction directly by coupling to H2oxidation.
Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Food and Food Products of Poultry Origin in Germany
Authors: Feßler Andrea T. , Kadlec Kristina , Hassel Melanie , Hauschild Tomasz , Eidam Christopher , Ehricht Ralf , Monecke Stefan , Schwarz Stefan
Published: July 2011

During a survey of fresh chicken and turkey meat as well as chicken and turkey meat products for the presence of methicillin-resistant
Staphylococcus aureus
(MRSA) isolates in Germany, 32 (37.2%) of 86 samples were MRSA positive. Twenty-eight of these MRSA isolates belonged to clonal complex 398 (CC398), which is widespread among food-producing animals. These CC398 isolates carried SCC
mec
elements of type IV or V and exhibited
spa
type t011, t034, t899, t2346 or t6574 and either the known
dru
types dt2b, dt6j, dt10a, dt10q, dt11a, dt11v, and dt11ab or the novel
dru
types dt6m, dt10as, and dt10at. In addition, two MRSA sequence type 9 (ST9) isolates with a type IV SCC
mec
cassette,
spa
type t1430, and
dru
type dt10a as well as single MRSA ST5 and ST1791 isolates with a type III SCC
mec
cassette,
spa
type t002, and
dru
type dt9v were identified. All but two isolates were classified as multiresistant. A wide variety of resistance phenotypes and genotypes were detected. All isolates were negative for the major virulence factors, such as Panton-Valentine leukocidin, toxic shock syndrome toxin 1, or exfoliative toxins. In contrast to the MRSA CC398 isolates, the four ST9, ST5, or ST1791 isolates harbored the
egc
gene cluster for enterotoxin G, I, M, N, O, and U genes. Although the relevance of contamination of fresh poultry meat or poultry products with MRSA is currently unclear, the presence of multiresistant and, in part, enterotoxigenic MRSA emphasizes the need for further studies to elucidate possible health hazards for consumers.
Genomic and Metabolic Profiling of Nonulosonic Acids in Vibrionaceae Reveal Biochemical Phenotypes of Allelic Divergence in Vibrio vulnificus
Authors: Lewis Amanda L. , Lubin Jean-Bernard , Argade Shilpa , Naidu Natasha , Choudhury Biswa , Boyd E. Fidelma
Published: July 2011

Nonulosonic acids (NulOs) encompass a large group of structurally diverse nine-carbon backbone α-keto sugars widely distributed among the three domains of life. Mammals express a specialized version of NulOs called sialic acids, which are displayed in prominent terminal positions of cell surface and secreted glycoconjugates. Within bacteria, the ability to synthesize NulOs has been demonstrated in a number of human pathogens and is phylogenetically widespread. Here we examine the distribution, diversity, evolution, and function of NulO biosynthesis pathways in members of the family
Vibrionaceae
. Among 27 species of
Vibrionaceae
examined at the genomic level, 12 species contained
nab
gene clusters. We document examples of duplication, divergence, horizontal transfer, and recombination of
nab
gene clusters in different
Vibrionaceae
lineages. Biochemical analyses, including mass spectrometry, confirmed that many species do, in fact, produce di-N-acetylated NulOs. A library of clinical and environmental isolates of
Vibrio vulnificus
served as a model for further investigation of
nab
allele genotypes and levels of NulO expression. The data show that lineage I isolates produce about 20-fold higher levels of NulOs than lineage II isolates. Moreover,
nab
gene alleles found in a subset of
V. vulnificus
clinical isolates express 40-fold higher levels of NulOs than
nab
alleles associated with environmental isolates. Taken together, the data implicate the family
Vibrionaceae
as a “hot spot” of NulO evolution and suggest that these molecules may have diverse roles in environmental persistence and/or animal virulence.
Semicontinuous Culture of Magnetospirillum gryphiswaldense MSR-1 Cells in an Autofermentor by Nutrient-Balanced and Isosmotic Feeding Strategies
Authors: Zhang Yang , Zhang Xiaojuan , Jiang Wei , Li Ying , Li Jilun
Published: July 2011

An improved strategy was developed for the high-density culture of
Magnetospirillum gryphiswaldense
strain MSR-1 and large-scale magnetosome production in both 7.5- and 42-liter autofermentors. By using a nutrient-balanced feeding strategy and the replacement of carbon and nitrogen sources to reduce accumulation of Na
+
and Cl
−
ions, we reduced the factors that tend to inhibit cell growth, particularly the increase of osmotic potential. Semicontinuous culture was thereby achieved in the autofermentor for the first time. When the cells were harvested at 36 and 73 h, magnetosome yields (dry weight) as high as 168.3 and 83.5 mg/liter/day, respectively, were achieved. These values were, respectively, approximately 10 and 5 times higher than the yields achieved in previous studies and represent a significant improvement in magnetosome production efficiency.
Calcineurin Colocalizes with P-Bodies and Stress Granules during Thermal Stress in Cryptococcus neoformans
Authors: Kozubowski Lukasz , Aboobakar Eanas F. , Cardenas Maria E. , Heitman Joseph
Published: July 2011

Calcineurin is a calcium-calmodulin-activated serine/threonine-specific phosphatase that operates during cellular responses to stress and plays a prominent role in transcriptional control, whereas regulatory events beyond transcription are less well characterized. This study reveals a novel transcription-independent role of calcineurin during the temperature stress response in the human fungal pathogen
Cryptococcus neoformans.
The diffusely cytoplasmic calcineurin catalytic subunit Cna1 relocates to endoplasmic reticulum (ER)-associated puncta and the mother-bud neck when cells are subjected to 37°C. More than 50% of Cna1 puncta contain the P-body constituent decapping enzyme Dcp1 and the stress granule constituent poly(A)-binding protein Pub1. These results support a model in which calcineurin orchestrates thermal stress responses by associating with sites of mRNA processing.
Bile Salts Induce Resistance to Polymyxin in Enterohemorrhagic Escherichia coliO157:H7
Authors: Kus Julianne V. , Gebremedhin Ahferom , Dang Vica , Tran Seav-Ly , Serbanescu Anca , Foster Debora Barnett
Published: July 2011

Many enteric bacteria use bile as an environmental cue to signal resistance and virulence gene expression. Microarray analysis of enterohemorrhagic
Escherichia coli
O157:H7 (EHEC) treated with bile salts revealed upregulation of genes for an efflux system (
acrAB
), a two-component signal transduction system (
basRS
/
pmrAB
), and lipid A modification (
arnBCADTEF
and
ugd
). Bile salt treatment of EHEC produced a
basS
- and
arnT
-dependent resistance to polymyxin.
A Novel Toxin Regulator, the CPE1446-CPE1447 Protein Heteromeric Complex, Controls Toxin Genes in Clostridium perfringens
Authors: Obana Nozomu , Nakamura Kouji
Published: July 2011

Clostridium perfringens
is a Gram-positive anaerobic spore-forming bacterium that is widespread in environmental soil and sewage, as well as in animal intestines. It is also a causative agent of diseases in humans and other animals, and it produces numerous extracellular enzymes and toxins. Although these toxins have been characterized in detail, regulators of toxin genes are less well understood. The present study identified CPE1447 and CPE1446 as novel regulators of toxin gene expression. CPE1447 and CPE1446 are cotranscribed as an operon, and the encoded proteins have a helix-turn-helix (HTH) motif at the N termini of their amino acid sequences, suggesting that CPE1447 and CPE1446 control the target genes as transcriptional regulators. The expression of several genes encoding toxins was changed in both a CPE1446 mutant and a CPE1447-CPE1446 deletion mutant. Complementation of CPE1446 and CPE1447 revealed that CPE1447 and CPE1446 coordinately regulate their target genes. CPE1447 protein was coprecipitated with His-tagged CPE1446 protein, indicating that the CPE1447 and CPE1446 proteins form a stable complex in
C. perfringens
under their native conditions. Although the small RNA that regulates several genes under the VirR/VirS two-component system (VR-RNA) positively affected CPE1447-CPE1446 mRNA expression, it did not control expression of the CPE1447-CPE1446 regulon, demonstrating that CPE1447 and CPE1446 regulate a different set of toxin genes from the VirR/VirS–VR-RNA cascade.
CT406 Encodes a Chlamydial Ortholog of NrdR, a Repressor of Ribonucleotide Reductase
Authors: Case Elizabeth Di Russo , Akers Johnny C. , Tan Ming
Published: July 2011

Chlamydia trachomatis
is an obligate intracellular bacterium that is dependent on its host cell for nucleotides.
Chlamydia
imports ribonucleotide triphosphates (NTPs) but not deoxyribonucleotide triphosphates (dNTPs) and instead uses ribonucleotide reductase to convert imported ribonucleotides into deoxyribonucleotides for DNA synthesis. The genes encoding ribonucleotide reductase have been recently shown to be negatively controlled by a conserved regulator called NrdR. In this study, we provide direct evidence that
Escherichia coli
NrdR is a transcriptional repressor and that
C. trachomatis
CT406 encodes its chlamydial ortholog. We showed that CT406 binds specifically to two NrdR boxes upstream of the
nrdAB
operon in
C. trachomatis
. Using an
in vitro
transcription assay, we confirmed that these NrdR boxes function as an operator since they were necessary and sufficient for CT406-mediated repression. We validated our
in vitro
findings with reporter studies in
E. coli
showing that both
E. coli
NrdR and CT406 repressed transcription from the
E. coli
nrdH
and
C. trachomatis
nrdAB
promoters
in vivo
. This
in vivo
repression was reversed by hydroxyurea treatment. Since hydroxyurea inhibits ribonucleotide reductase and reduces intracellular deoxyribonucleotide levels, these results suggest that NrdR activity is modulated by a deoxyribonucleotide corepressor.
UvrD2 Is Essential in Mycobacterium tuberculosis, but Its Helicase Activity Is Not Required
Authors: Williams Alan , Güthlein Carolin , Beresford Nicola , Böttger Erik C. , Springer Burkhard , Davis Elaine O.
Published: July 2011

UvrD is an SF1 family helicase involved in DNA repair that is widely conserved in bacteria.
Mycobacterium tuberculosis
has two annotated UvrD homologues; here we investigate the role of UvrD2. The
uvrD2
gene at its native locus could be knocked out only in the presence of a second copy of the gene, demonstrating that
uvrD2
is essential. Analysis of the putative protein domain structure of UvrD2 shows a distinctive domain architecture, with an extended C terminus containing an HRDC domain normally found in SF2 family helicases and a linking domain carrying a tetracysteine motif. Truncated constructs lacking the C-terminal domains of UvrD2 were able to compensate for the loss of the chromosomal copy, showing that these C-terminal domains are not essential. Although UvrD2 is a functional helicase, a mutant form of the protein lacking helicase activity was able to permit deletion of
uvrD2
at its native locus. However, a mutant protein unable to hydrolyze ATP or translocate along DNA was not able to compensate for lack of the wild-type protein. Therefore, we concluded that the essential role played by UvrD2 is unlikely to involve its DNA unwinding activity and is more likely to involve DNA translocation and, possibly, protein displacement.
A Novel Testosterone Catabolic Pathway in Bacteria
Authors: Leu Yann-Lii , Wang Po-Hsiang , Shiao Ming-Shi , Ismail Wael , Chiang Yin-Ru
Published: July 2011

Forty years ago, Coulter and Talalay (A. W. Coulter and P. Talalay, J. Biol. Chem. 243:3238–3247, 1968) established the oxygenase-dependent pathway for the degradation of testosterone by aerobes. The oxic testosterone catabolic pathway involves several oxygen-dependent reactions and is not available for anaerobes. Since then, a variety of anaerobic bacteria have been described for the ability to degrade testosterone in the absence of oxygen. Here, a novel, oxygenase-independent testosterone catabolic pathway in such organisms is described.
Steroidobacter denitrificans
DSMZ18526 was shown to be capable of degrading testosterone in the absence of oxygen and was selected as the model organism in this study. In a previous investigation, we identified the initial intermediates involved in an anoxic testosterone catabolic pathway, most of which are identical to those of the oxic pathway demonstrated in
Comamonas testosteroni
. In this study, five additional intermediates of the anoxic pathway were identified. We demonstrated that subsequent steps of the anoxic pathway greatly differ from those of the established oxic pathway, which suggests that a novel pathway for testosterone catabolism is present. In the proposed anoxic pathway, a reduction reaction occurs at C-4 and C-5 of androsta-1,4-diene-3,17-dione, the last common intermediate of both the oxic and anoxic pathways. After that, a novel hydration reaction occurs and a hydroxyl group is thus introduced to the C-1α position of C
19
steroid substrates. To our knowledge, an enzymatic hydration reaction occurring at the A ring of steroid compounds has not been reported before.
A Specialized Aspartokinase Enhances the Biosynthesis of the Osmoprotectants Ectoine and Hydroxyectoine in Pseudomonas stutzeriA1501
Authors: Stöveken Nadine , Pittelkow Marco , Sinner Tatjana , Jensen Roy A. , Heider Johann , Bremer Erhard
Published: July 2011

The compatible solutes ectoine and hydroxyectoine are widely produced by bacteria as protectants against osmotic and temperature stress.l-Aspartate-beta-semialdehyde is used as the precursor molecule for ectoine/hydroxyectoine biosynthesis that is catalyzed by the EctABCD enzymes.l-Aspartate-beta-semialdehyde is a central intermediate in different biosynthetic pathways and is produced froml-aspartate by aspartokinase (Ask) and aspartate-semialdehyde-dehydrogenase (Asd). Ask activity is typically stringently regulated by allosteric control to avoid gratuitous synthesis of aspartylphosphate. Many organisms have evolved multiple forms of aspartokinase, and feedback regulation of these specialized Ask enzymes is often adapted to the cognate biochemical pathways. The ectoine/hydroxyectoine biosynthetic genes (ectABCD) are followed in a considerable number of microorganisms by anaskgene (ask_ect), suggesting that Ask_Ect is a specialized enzyme for this osmoadaptive biosynthetic pathway. However, none of these Ask_Ect enzymes have been functionally characterized.Pseudomonas stutzeriA1501 synthesizes both ectoine and hydroxyectoine in response to increased salinity, and it possesses two Ask enzymes: Ask_Lys and Ask_Ect. We purified both Ask enzymes and found significant differences with regard to their allosteric control: Ask_LysC was inhibited by threonine and in a concerted fashion by threonine and lysine, whereas Ask_Ect showed inhibition only by threonine. TheectABCD_askgenes fromP. stutzeriA1501 were cloned and functionally expressed inEscherichia coli, and this led to osmostress protection. AnE. colistrain carrying the plasmid-basedectABCD_askgene cluster produced significantly more ectoine/hydroxyectoine than a strain expressing theectABCDgene cluster alone. This finding suggests a specialized role for Ask_Ect in ectoine/hydroxyectoine biosynthesis.
Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190
Authors: Sales Christopher M. , Mahendra Shaily , Grostern Ariel , Parales Rebecca E. , Goodwin Lynne A. , Woyke Tanja , Nolan Matt , Lapidus Alla , Chertkov Olga , Ovchinnikova Galina , Sczyrba Alexander , Alvarez-Cohen Lisa
Published: July 2011

Pseudonocardia dioxanivorans
CB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus
Pseudonocardia
for which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants.
Transcriptional Profiling of Nitrogen Fixation in Azotobacter vinelandii
Authors: Hamilton Trinity L. , Ludwig Marcus , Dixon Ray , Boyd Eric S. , Dos Santos Patricia C. , Setubal João C. , Bryant Donald A. , Dean Dennis R. , Peters John W.
Published: July 2011

Most biological nitrogen (N
2
) fixation results from the activity of a molybdenum-dependent nitrogenase, a complex iron-sulfur enzyme found associated with a diversity of bacteria and some methanogenic archaea.
Azotobacter vinelandii
, an obligate aerobe, fixes nitrogen via the oxygen-sensitive Mo nitrogenase but is also able to fix nitrogen through the activities of genetically distinct alternative forms of nitrogenase designated the Vnf and Anf systems when Mo is limiting. The Vnf system appears to replace Mo with V, and the Anf system is thought to contain Fe as the only transition metal within the respective active site metallocofactors. Prior genetic analyses suggest that a number of
nif
-encoded components are involved in the Vnf and Anf systems. Genome-wide transcription profiling of
A. vinelandii
cultured under nitrogen-fixing conditions under various metal amendments (e.g., Mo or V) revealed the discrete complement of genes associated with each nitrogenase system and the extent of cross talk between the systems. In addition, changes in transcript levels of genes not directly involved in N
2
fixation provided insight into the integration of central metabolic processes and the oxygen-sensitive process of N
2
fixation in this obligate aerobe. The results underscored significant differences between Mo-dependent and Mo-independent diazotrophic growth that highlight the significant advantages of diazotrophic growth in the presence of Mo.
Synergism between Different Germinant Receptors in the Germination of Bacillus subtilis Spores
Authors: Yi Xuan , Liu Jintao , Faeder James R. , Setlow Peter
Published: July 2011

Rates of commitment to germinate and germination of
Bacillus subtilis
spores with mixtures of low concentrations of germinants acting on different germinant receptors (GRs) were much higher than the sums of the rates of commitment and germination with individual germinants alone. This synergism with mixtures of nutrient germinants was not seen with spores lacking GRs responsible for recognizing one or several components of the germinant mixtures and was not eliminated by either a
gerD
mutation or overexpression of one of the GRs involved in this synergism. This synergism was also not seen between the germinant
l
-valine, which acts via a GR, and the germinant dodecylamine, which does not act via any GR. These results indicate that spores not only integrate but can also amplify signals from multiple germinants and multiple GRs in determining rates of commitment and overall spore germination. This amplification can be explained by a simple mechanism in which a single signal integrator triggers germination above an accumulation threshold. Direct cooperative action between GRs may further add to the synergism seen in germination triggered by multiple GRs. Further experiments and modeling are required to determine the relative contributions of these different mechanisms.
Escherichia coliNucleoside Diphosphate Kinase Mutants Depend on Translesion DNA Synthesis To Prevent Mutagenesis
Authors: Nordman Jared , Wright Andrew
Published: July 2011

Escherichia coli
nucleoside diphosphate (NDP) kinase mutants have an increased frequency of spontaneous mutation, possibly due to uracil misincorporation into DNA. Here we show that NDP kinase mutants are dependent on translesion DNA synthesis, often a mutagenic form of DNA synthesis, to prevent mutagenesis.
Neighbourhood street connectivity and injury in youth: a national study of built environments in Canada
Authors: Mecredy Graham , Janssen Ian , Pickett William
Published: July 2011

Background

The influence of the built environment on health is of contemporary societal interest. The design of streets in neighbourhood settings may contribute positively to the health of populations through increased physical activity, but it may also have injury consequences.

Methods

We conducted a national cross-sectional study to describe the injury experiences of 9021 students from 180 Canadian schools that participated in the 2006 Health Behaviour in School-Aged Children survey. Street designs surrounding each school (5 km circular buffer) were estimated via geographic information systems for three established measures of connectivity (intersection density, average block length and connected node ratio). A composite scale of connectivity was derived using factor analysis. Multilevel logistic regression analyses were used to examine the associations between the composite connectivity measure and students' reports of physical activity injuries occurring in the street (street injuries).

Results

Students living in neighbourhoods with low versus high street connectivity reported possible increases in the occurrence of street injuries (OR, 1.38; 95% CI, 0.84 to 2.26). This relationship was mainly attributable to the occurrence of bicycle injuries (52% of all street injuries; OR, 2.33; 95% CI, 1.28 to 4.25). The population attributable risk was 20% for street injuries potentially caused by living in an area with low connectivity.

Conclusion

The design of streets, as a measure of the built environment, is related to the occurrence of youth injury. Positive effects of poorly connected street designs that are likely in terms of physical activity were offset by negative injury outcomes, although the injuries observed were mostly minor in nature.
PAI-1 expression and its regulation by promoter 4G/5G polymorphism in clear cell renal cell carcinoma
Authors: Choi Jung-Woo , Lee Ju-Han , Park Hong Seok , Kim Young-Sik
Published: July 2011

Aims

To characterise patients with high plasminogen activator inhibitor-1 (PAI-1) expression as oral PAI-1 antagonists are currently in preclinical trials, and to determine whether thePAI-1promoter 4G/5G polymorphism regulates PAI-1 expression in clear cell renal cell carcinoma (CCRCC).

Methods

PAI-1 expression was examined by immunohistochemistry in 69 CCRCC specimens. In addition, the promoter 4G/5G polymorphism was investigated by both allele-specific PCR and direct DNA sequencing.

Results

PAI-1 was overexpressed in 25/69 (36.2%) patients with CCRCC. PAI-1 staining was intense in tumour cells with a high Fuhrman nuclear grade and in spindle-shaped tumour cells. PAI‐1 expression was significantly associated with older age at diagnosis (p=0.027), high nuclear grade (p<0.001), advanced clinical stage (p=0.030) and distant metastasis (p=0.009). In survival analyses, PAI-1 expression was correlated with disease-free survival in Kaplan–Meier curves (p=0.015) but was not significant in the Cox hazards model (p=0.527). The frequencies of the promoter polymorphism were 24.6% (17/69) 4G/4G, 43.5% (30/69) 4G/5G and 31.9% (22/69) 5G/5G. The homozygous 4G/4G or 5G/5G group showed a tendency for a high nuclear grade (p=0.05) but the 4G/5G polymorphism was not related to other prognostic parameters. PAI-1 expression was poorly correlated with its promoter 4G/5G polymorphism (Spearman ρ=0.088).

Conclusions

CCRCC with high PAI-1 expression is characterised by older age, high nuclear grade, advanced stage, distant metastasis and/or shortened disease-free survival. PAI-1 expression is not affected by the promoter 4G/5G polymorphism.
BCL-6 expression in mesenchymal tumours: an immunohistochemical and fluorescence in situ hybridisation study
Authors: Walters Matthew P , McPhail Ellen D , Law Mark E , Folpe Andrew L
Published: July 2011

The BCL-6 proto-oncogene encodes a transcriptional repressor protein. Among normal tissues, BCL-6 expression is confined to germinal center B-cells and a subpopulation of T-helper cells. Little is known about BCL-6 expression in mesenchymal tissues. We examined a series of solitary fibrous tumor (SFT) and other mesenchymal tumors for BCL-6 expression. Immunohistochemistry for BCL-6 was performed on 64 mesenchymal tumors [26 SFT (19 benign/uncertain, 7 malignant), 6 synovial sarcomas (SS), 5 gastrointestinal stromal tumors (GIST), 5 malignant peripheral nerve sheath tumors (MPNST), 5 leiomyosarcomas (LMS), 9 leiomyomas (LM) 4 desmoid tumors (DT), 4 perineuriomas (PN)]. Nuclear immunoreactivity was considered positive. Six BCL-6 positive SFT were also tested for BCL-6 gene rearrangement/amplification by FISH. Nuclear expression of BCL-6 was seen in 13/26 SFT, 5/5 LMS, 1/9 LM, 5/6 SS, 1/5 GIST, 1/5 MPNST, 1/4 PN, and 0/5 DT. BCL-6 expression was significantly more frequent in malignant (6/7) as compared with benign/uncertain SFT (6/19) (p=0.02) and in LMS (5/5) as compared with LM (1/9) (p=0.003). FISH for BCL-6 rearrangement/amplification was negative in all tested cases. We have observed BCL-6 expression in 50% or more of SFT, SS, and LMS, and in a lesser percentage of LM, GIST, MPNST and PN. Significantly more frequent expression of BCL-6 in malignant compared with benign/uncertain SFT and in LMS compared with LM suggests abnormalities in the BCL-6 signaling pathway may contribute to malignant transformation in at least some mesenchymal tumors. It is unlikely that BCL-6 expression in mesenchymal tumors is due to BCL-6 gene amplification or rearrangement. amplification or rearrangement.
Assessment of long-term and recent pesticide exposure among rural school children in Nicaragua
Authors: Rodríguez Teresa , van Wendel de Joode Berna , Lindh Christian H , Rojas Marianela , Lundberg Ingvar , Wesseling Catharina
Published: July 2011

Objective

This study assessed pesticide exposure of children in rural Nicaragua in relation to parental pesticide use, from around conception to current school age, as part of an epidemiological evaluation of neurodevelopment effects.

Methods

We included 132 children whose parents were subsistence farmers or plantation workers, or had an agricultural history. As proxies for children's long-term exposures, we constructed cumulative parental pesticide-specific use indices for periods before and after the child's birth from data obtained using an icon-calendar-based questionnaire, of application hours (h) for plantation workers and subsistence farmers, and of kilograms of active ingredients (ai) only for subsistence farmers. Pesticide residues of TCPY, 3-PBA and 2,4-D were analysed in children's urine as indicators for current exposures.

Results

Life-time indices were highest for the organophosphates chlorpyrifos (median 114 h (min 2; max 1584), 19.2 kg ai (min 0.37; max 548)) and methamidophos (84 h (6; 1964), 12.2 kg ai (0.30; 780)). The P50 values of children's urinary residues were 3.7 μg/g creatinine for TCPY, 2.8 for 3-PBA and 0.9 for 2,4-D; TCPY values are comparable with those in other countries, but 3-PBA and 2,4-D are considerably higher. The maximum levels for all three pesticides are the highest reported for children. Residues increased on days after application, but most high residue levels were unrelated to parental pesticide applications.

Conclusion

Urinary pesticide residues reveal high environmental exposure among children in rural Nicaragua. The quantitative parental pesticide use indices as proxies for children's exposures during different periods may be useful for the evaluation of developmental health effects.
SPEED OF LAST VEHICLE FEEDBACK STRATEGY IN INTELLIGENT TRANSPORTATION SYSTEMS
Authors: CHEN BOKUI , CHEN MENGSU , ZHANG ZILING , XIE YANBO , WANG BINGHONG
Published: July 2011

Traffic jam has become a big problem in the development of economy. How to effectively improve the road capacity is becoming the key problem in the research of traffic flow. As the core part of the next generation intelligent transportation systems, the feedback strategy has attracted much attention. In recent years, researchers have proposed many effective strategies. In this paper, a strategy called speed of last vehicle feedback strategy is introduced, and simulated in a two-route scenario with one exit. Result shows that compared with other strategies, this strategy has certain advantages on average flux — a criteria describing traffic capacity of traffic systems. More importantly, the implementation of this strategy is very simple.
DETERMINANTS OF TERRORISM: A PANEL DATA ANALYSIS OF SELECTED SOUTH ASIAN COUNTRIES
Authors: NASIR MUHAMMAD , ALI AMANAT , REHMAN FAIZ UR
Published: July 2011

The phenomenon of terrorism has riveted world's unwavering attention since 9/11. The underlying study investigates the determinants of terrorism in the South Asian region. Applying negative binomial regression, the study finds that both political structure and economic conditions are responsible for terrorism. On the economic front, relative deprivation represented by income disparity is the major cause of terrorism. On the other hand, deprivation of the people of their political rights and civil liberties, exhibited by political repression, compels them to be involved in terrorist activities. Our findings illustrates that high literacy rate is one of the foremost reason for terrorism in the region.
DIFFERENTIAL OUTPUT ELASTICITY OF EMPLOYMENT DURING POST-ECONOMIC REFORM PERIOD IN THE INDIAN ECONOMY
Authors: UPENDER M.
Published: July 2011

This paper investigates the sign and size of the differential output elasticity of employment for different industries in the private and public organized sectors of the Indian economy during post-economic reform period. A logarithmic form of demand function for employment, derived from the constant elasticity of substitution production function is estimated. An interaction variable is introduced after having ensured that the employment function has a structural shift by Chow break test. The results based on the time series data from the period 1969–1970 to 2004–2005, show that the positive magnitude of elasticity of employment with respect to output in transport, storage and communications industry is relatively very high, as the differential output elasticity of employment is not only positive but also more than unity followed by wholesale and retail trade and financing, insurance and real estate industries in the private organized sector during the post-economic reform period. This reflects the fact that the labor absorption capacity in the industries of transport, storage and communications, wholesale and retail, financing, insurance and real estate is relatively high. The magnitude of output elasticity of employment in financing, insurance and real estate is relatively high during the post-economic reform period as the differential output elasticity of employment is relatively small as compared to output elasticity of employment during the pre-economic reform period. The labor absorption capacity in private sector during the post-reform period is found to be relatively high as compared to public sector as the differential employment elasticity during the post-reform period in private sector is low. Further the results for the organized sector as a whole illustrate that the output elasticity of employment during the post-reform period is negative on account of negative differential output elasticity of employment showing that the economic growth during the post-reform period is not labor intensive in the Indian economy. Therefore, there is a need to review the sectoral policies to generate additional employment opportunities in the organised sector of the Indian economy.
TIME-DEPENDENT SOLUTIONS OF 5D VACUUM EINSTEIN EQUATIONS WITH COSMOLOGICAL CONSTANT
Authors: LEE TAE HOON
Published: July 2011

We solve vacuum field equations in five-dimensional gravity with cosmological constant to determine the time-dependence of the Robertson–Walker scale factor. We discuss its cosmological implications.
AN EXPERIMENTAL STUDY ON THE TRANSIENT TEMPERATURE TEST OF THE PLANETARY GEAR REDUCER OF THE EPBM
Authors: CHEN LIFENG , WU XIAOLING , QIN DATONG , WEN ZEJUN
Published: July 2011

A temperature test apparatus has been designed to measure the temperature rise of the planetary gear train. The experimental platform integrated the temperature test system, siemens operating system and industrial personal computer (IPC). The temperatures of various locations have been investigated under rated condition and the oil temperature-rise time under different speed was estimated. The experimental results indicated that the temperatures of the super-speed planetary gear train (PGT) of the earth pressure balance shield machine (EPBM) rise quickly than the low-speed PGT and the speed has significant influence on the temperature of the PGT. Through comparison the oil temperatures under reverse direction and forward direction, the direction of the motor has little influence on the temperature of the PGT.
STUDY AND APPLICATION OF OPEN DIE FORGING CAPP SYSTEM BASED ON PROCESS KNOWLEDGE
Authors: KONG FANXIN , ZUO JIANMIN , ZHA GUANGCHENG , ZHANG JIAO
Published: July 2011

This paper discusses concepts and methods related to CAPP (Computer Aided Process Planning) system based on process knowledge. The CAPP system framework module of Open Die Forging facing industry is proposed. This module can realize the fusion of retrieval type, derived type, and creative type, etc. CAPP functions, reasons and makes decision based on knowledge and, develops the optimal process route, and process card. In this paper, the main functions of the system are introduced based on developments of open die forging CAPP system in recent years.
RESEARCH ON BUSINESS PROCESS MANAGEMENT-BASED SUPPLY CHAIN SYSTEM
Authors: YU XIN , LIANG CHENGSHENG , LI SHUFEN , SUN XUE
Published: July 2011

Supply chain management provides a new kind of enterprise relationship management for ensuring the survival and development of enterprises in modern market competition, but with the development of business, information explosion, and the acceleration of business globalization, supply chain management will become increasingly complex. This article provides a method to construct the enterprise supply chain systems from the perspective of the business process management. It utilizes service-oriented architecture to achieve the componentization of each business unit, which makes chain system adapt to the changes of business processes rapidly and deploy these changes into IT system. Ultimately, IT systems can respond to supply chain system in time and then reduce operation costs and time when enterprise is carrying out business restructuring and process optimization.
RESEARCH ON DIGITAL MODEL QUALITY CHECK SYSTEM BASED ON KNOWLEDGE ENGINEERING
Authors: LIU DEFANG , LI LIYING , ZHOU LINZHEN , WANG BIN
Published: July 2011

This paper developed a quality check system for digital model based on knowledge engineering and explained the frame construction of the check system. The workflow and rules of digital model check were expressed in detail by bringing in knowledge engineering. Digital model quality check process was divided into five steps: system environment check, general data check, entity model check, assembly model check, and engineering drawing check. This Check System will contribute to collecting data from high-qualified models and supporting the product for designing and manufacturing. Finally, a case was employed to demonstrate the efficiency and feasibility of the quality check system for digital models.
RESEARCH ON DESIGN METHOD OF DEMAND-DRIVEN PRODUCT CONFIGURATION FOR MASS CUSTOMIZATION
Authors: WANG YAPING , HAN GUIHUA , GE JIANGHUA , QI JINGRUI , XU JIANYUAN
Published: July 2011

This paper proposed demand-driven personalized product configuration design method. A variety of customer orders were clustered and fuzzy transformed; using ontology's feature to establish customer demand ontology model; in order to enable the product family to meet the dynamic demand of customers, established mapping relationship of customer demands and product family; using ontology to express product family model, achieved mapping of customer needs ontology and product family ontology, and improved efficiency of product configuration. Finally, we take planetary reducer as an example to demonstrate the feasibility of the method.
SIMULATION ON THE GROUND WAFER SHAPE IN WAFER ROTATIONAL GRINDING
Authors: TANG KEYAN , KANG RENKE
Published: July 2011

During the wafer rotational grinding, the wafer is located on a porous ceramic vacuum chuck, so there are many factors that can affect the wafer shape in the process of the wafer grinding. The wafer shape has an important influence on the surface quality of the silicon wafer and it will be greatly different if the processing parameters are different. So in this paper, based on a mathematics model of the ground wafer shape which has been developed, a simulation system of the wafer shape was made out by using Visual C++ and OpenGL. The relationship between the parameters and the wafer shape was researched and analyzed. The simulation results showed that the roll angle and the pitch angle had the greatest impact on the wafer shape. And the simulation results with different parameters have been compared with each other for the final conclusions. So the results demonstrate the mathematics model is reasonable and the simulation system is of high simulating accuracy, and the ground wafer shape can be predicted very well by it. The research results are significant to logically choose the wafer grinding parameters and effectively control the ground wafer shape.
THE CASE-BASED REASONING TECHNOLOGY BASED ON FUNCTIONAL MODE
Authors: LI PEIGANG , FENG XIANYING , SONG YAQING
Published: July 2011

The conceptual design of products is an important stage in the design process. However, how to reuse the existing and successful parts is always the key factor to the success of products in the process. To match the case parts rapidly and accurately, this paper puts forward the case-based reasoning (CBR) technology based on functional mode, which expresses accurately the functional structure through the generalized positioning of parts in products. Also, the scheme of variable-length hierarchical coding of functional mode is proposed, and the analytic hierarchy process (AHP) is adopted to determine matching function. Then, based on the hierarchy retrieval mode, the accurate matching of case parts is realized. The application of instance shows that the matching mode is feasible.
SHARPER TOTAL VARIATION BOUNDS FOR THE P-SYSTEM OF FLUID DYNAMICS
Authors: TSIKKOU CHARIS
Published: July 2011

For the p-system of fluid dynamics and under the assumption that the initial data have small oscillation but not necessarily small total variation, we reproduce the so-called Glimm–Lax estimates with greater accuracy. Our approach recovers the results known for smooth flux functions, and is based on the theory of generalized characteristics and Dafermos' technique of polygonal approximations.
SOLUTIONS OF QUASI-LINEAR WAVE EQUATIONS POLYHOMOGENEOUS AT NULL INFINITY IN HIGH DIMENSIONS
Authors: CHRUŚCIEL PIOTR T. , WAFO ROGER TAGNE
Published: July 2011

We prove propagation of weighted Sobolev regularity for solutions of the hyperboloidal Cauchy problem for a class of quasi-linear symmetric hyperbolic systems, under structure conditions compatible with the Einstein–Maxwell equations in space-time dimensions n + 1 ≥ 7. Similarly we prove propagation of polyhomogeneity in dimensions n + 1 ≥ 9. As a byproduct we obtain, in those last dimensions, polyhomogeneity at null infinity of small data solutions of vacuum Einstein, or Einstein–Maxwell equations evolving out of initial data which are stationary outside of a ball.
A constituent-based model of age-related changes in conduit arteries
Authors: Tsamis Alkiviadis , Rachev Alexander , Stergiopulos Nikos
Published: July 2011

In the present report, a constituent-based theoretical model of age-related changes in geometry and mechanical properties of conduit arteries is proposed. The model was based on the premise that given the time course of the load on an artery and the accumulation of advanced glycation end-products in the arterial tissue, the initial geometric dimensions and properties of the arterial tissue can be predicted by a solution of a boundary value problem for the governing equations that follow from finite elasticity, structure-based constitutive modeling within the constrained mixture theory, continuum damage theory, and global growth approach for stress-induced structure-based remodeling. An illustrative example of the age-related changes in geometry, structure, composition, and mechanical properties of a human thoracic aorta is considered. Model predictions were in good qualitative agreement with available experimental data in the literature. Limitations and perspectives for refining the model are discussed.