bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of Yeast and Bacterial Gene Transcripts in Retail Cheeses by Reverse Transcription-Quantitative PCR
Authors: Monnet Christophe , Straub Cécile , Castellote Jessie , Onesime Djamila , Bonnarme Pascal , Irlinger Françoise
Published: November 2012

The cheese microbiota contributes to a large extent to the development of the typical color, flavor, and texture of the final product. Its composition is not well defined in most cases and varies from one cheese to another. The aim of the present study was to establish procedures for gene transcript quantification in cheeses by reverse transcription-quantitative PCR. Total RNA was extracted from five smear-ripened cheeses purchased on the retail market, using a method that does not involve prior separation of microbial cells. 16S rRNA and malate:quinone oxidoreductase gene transcripts of
Corynebacterium casei
,
Brevibacterium aurantiacum
, and
Arthrobacter arilaitensis
and 26S rRNA and beta tubulin gene transcripts of
Geotrichum candidum
and
Debaryomyces hansenii
could be detected and quantified in most of the samples. Three types of normalization were applied: against total RNA, against the amount of cheese, and against a reference gene. For the first two types of normalization, differences of reverse transcription efficiencies from one sample to another were taken into account by analysis of exogenous control mRNA. No good correlation was found between the abundances of target mRNA or rRNA transcripts and the viable cell concentration of the corresponding species. However, in most cases, no mRNA transcripts were detected for species that did not belong to the dominant species. The applications of gene expression measurement in cheeses containing an undefined microbiota, as well as issues concerning the strategy of normalization and the assessment of amplification specificity, are discussed.
Enhanced Gene Detection Assays for Fumarate-Adding Enzymes Allow Uncovering of Anaerobic Hydrocarbon Degraders in Terrestrial and Marine Systems
Authors: von Netzer Frederick , Pilloni Giovanni , Kleindienst Sara , Krüger Martin , Knittel Katrin , Gründger Friederike , Lueders Tillmann
Published: November 2012

The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. Fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) have already been established as specific functional marker genes for anaerobic hydrocarbon degraders. Several recent studies based on pure cultures and laboratory enrichments have shown the existence of new and deeply branching FAE gene lineages, such as clostridial benzylsuccinate synthases and homologues, as well as naphthylmethylsuccinate synthases. However, established FAE gene detection assays were not designed to target these novel lineages, and consequently, their detectability in different environments remains obscure. Here, we present a new suite of parallel primer sets for detecting the comprehensive range of FAE markers known to date, including clostridial benzylsuccinate, naphthylmethylsuccinate, and alkylsuccinate synthases. It was not possible to develop one single assay spanning the complete diversity of FAE genes alone. The enhanced assays were tested with a range of hydrocarbon-degrading pure cultures, enrichments, and environmental samples of marine and terrestrial origin. They revealed the presence of several, partially unexpected FAE gene lineages not detected in these environments before: distinct deltaproteobacterial and also clostridialbssAhomologues as well as environmentalnmsAhomologues. These findings were backed up by dual-digest terminal restriction fragment length polymorphism diagnostics to identify FAE gene populations independently of sequencing. This allows rapid insights into intrinsic degrader populations and degradation potentials established in aromatic and aliphatic hydrocarbon-impacted environmental systems.
Persistence and Leaching Potential of Microorganisms and Mineral N in Animal Manure Applied to Intact Soil Columns
Authors: Amin M. G. Mostofa , Forslund Anita , Bui Xuan Thanh , Juhler René K. , Petersen Søren O. , Lægdsmand Mette
Published: November 2012

Pathogens may reach agricultural soils through application of animal manure and thereby pose a risk of contaminating crops as well as surface and groundwater. Treatment and handling of manure for improved nutrient and odor management may also influence the amount and fate of manure-borne pathogens in the soil. A study was conducted to investigate the leaching potentials of a phage (Salmonella entericaserovar Typhimurium bacteriophage 28B) and two bacteria,Escherichia coliandEnterococcusspecies, in a liquid fraction of raw pig slurry obtained by solid-liquid separation of this slurry and in this liquid fraction after ozonation, when applied to intact soil columns by subsurface injection. We also compared leaching potentials of surface-applied and subsurface-injected raw slurry. The columns were exposed to irrigation events (3.5-h period at 10 mm h−1) after 1, 2, 3, and 4 weeks of incubation with collection of leachate. By the end of incubation, the distribution and survival of microorganisms in the soil of each treatment and in nonirrigated columns with injected raw slurry or liquid fraction were determined.E. coliin the leachates was quantified by both plate counts and quantitative PCR (qPCR) to assess the proportions of culturable and nonculturable (viable and nonviable) cells. Solid-liquid separation of slurry increased the redistribution in soil of contaminants in the liquid fraction compared to raw slurry, and the percent recovery ofE. coliandEnterococcusspecies was higher for the liquid fraction than for raw slurry after the four leaching events. The liquid fraction also resulted in more leaching of all contaminants exceptEnterococcusspecies than did raw slurry. Ozonation reducedE. colileaching only. Injection enhanced the leaching potential of the microorganisms investigated compared to surface application, probably because of a better survival with subsurface injection and a shorter leaching path.
Poly-γ-
d
-Glutamic Acid Capsule Interferes with Lytic Infection of Bacillus anthracis by B. anthracis-Specific Bacteriophages
Authors: Negus David , Burton Jane , Sweed Angela , Gryko Romuald , Taylor Peter W.
Published: November 2012

The poly-γ-
d
-glutamic acid capsule of
Bacillus anthracis
is a barrier to infection by
B. anthracis
-specific bacteriophages. Capsule expression was found to completely inhibit lytic infection by γ phage, an observation supported by the demonstration that this phage does not elaborate a hydrolase that would facilitate penetration through the protective capsule outer layer.
Occurrence of Virulence Genes Associated with Diarrheagenic Pathotypes in Escherichia coli Isolates from Surface Water
Authors: Sidhu Jatinder P. S. , Ahmed Warish , Hodgers Leonie , Toze Simon
Published: November 2012

Escherichia coli
isolates (
n
= 300) collected from six sites in subtropical Brisbane, Australia, prior to and after storm events were tested for the presence of 11 virulence genes (VGs) specific to diarrheagenic pathotypes. The presence of
eaeA
,
stx
1
,
stx
2
, and
ehxA
genes specific for the enterohemorrhagic
E. coli
(EHEC) pathotype was detected in 56%, 6%, 10%, and 13% of isolates, respectively. The VGs
astA
(69%) and
aggR
(29%), carried by enteroaggregative (EAEC) pathotypes, were frequently detected in
E. coli
isolates. The enteropathogenic
E. coli
(EPEC) gene
bfp
was detected in 24% of isolates. In addition, enteroinvasive
E. coli
(EIEC) VG
ipaH
was also detected in 14% of isolates. During dry periods, isolates belonging to the EAEC pathotype were most commonly detected (23%), followed by EHEC (11%) and EPEC (11%). Conversely, a more uniform prevalence of pathotypes, EPEC (14%), EAEC (12%), EIEC (10%), EHEC (7%), and ETEC (7%), was observed after the storm events. The results of this study highlight the widespread occurrence of potentially diarrheagenic pathotypes in the urban aquatic ecosystems. While the presence of VGs in
E. coli
isolates alone is insufficient to determine pathogenicity, the presence of diarrheagenic
E. coli
pathotypes in high frequency after the storm events could lead to increased health risks if untreated storm water were to be used for nonpotable purposes and recreational activities.
Cello-Oligosaccharide Oxidation Reveals Differences between Two Lytic Polysaccharide Monooxygenases (Family GH61) from Podospora anserina
Authors: Bey Mathieu , Zhou Simeng , Poidevin Laetitia , Henrissat Bernard , Coutinho Pedro M. , Berrin Jean-Guy , Sigoillot Jean-Claude
Published: November 2012

The genome of the coprophilic ascomycete
Podospora anserina
encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes (
P. anserina
GH61A [
Pa
GH61A] and
Pa
GH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in
Pichia pastoris
. Synergistic cooperation between
Pa
GH61A or
Pa
GH61B with the cellobiose dehydrogenase (CDH) of
Pycnoporus cinnabarinus
on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A striking difference between
Pa
GH61A and
Pa
GH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of
Pa
GH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a geminal diol group. The different properties of
Pa
GH61A and
Pa
GH61B and their effect on the interaction with CDH are discussed in regard to the proposed
in vivo
function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis.
Role of Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase in Visceral Organ Infection by Leishmania donovani
Authors: Zhang Wen-Wei , McCall Laura-Isobel , Matlashewski Greg
Published: November 2012

The initial 7 steps of the glycolytic pathway from glucose to 3-phosphoglycerate are localized in the glycosomes in
Leishmania
, including step 6, catalyzed by the enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In
L. donovani
and
L. mexicana
, there exists a second GAPDH enzyme present in the cytosol that is absent in
L. braziliensis
and that has become a pseudogene in
L. major.
To investigate the role of the cytosolic GAPDH (cGAPDH), an
L. donovani
cGAPDH-null mutant was generated, and conversely, the functional
L. donovani
cGAPDH was introduced into
L. major
and the resulting engineered parasites were characterized. The
L. donovani
cGAPDH-null mutant was able to proliferate at the same rate as the wild-type parasite in glucose-deficient medium. However, in the presence of glucose, the
L. donovani
cGAPDH-null mutant consumed less glucose and proliferated more slowly than the wild-type parasite and displayed reduced infectivity in visceral organs of experimentally infected mice. This demonstrates that cGAPDH is functional in
L. donovani
and is required for survival in visceral organs. Restoration of cGAPDH activity in
L. major
, in contrast, had an adverse effect on
L. major
proliferation in glucose-containing medium, providing a possible explanation of why it has evolved into a pseudogene in
L. major
. This study indicates that there is a difference in glucose metabolism between
L. donovani
and
L. major
, and this may represent an important factor in the ability of
L. donovani
to cause visceral disease.
White-Opaque Switching of Candida albicans Allows Immune Evasion in an Environment-Dependent Fashion
Authors: Sasse Christoph , Hasenberg Mike , Weyler Michael , Gunzer Matthias , Morschhäuser Joachim
Published: November 2012

Candida albicansstrains that are homozygous at the mating type locus can spontaneously and reversibly switch from the normal yeast morphology (white) to an elongated cell type (opaque), which is the mating-competent form of the fungus. White-opaque switching also influences the ability ofC. albicansto colonize and proliferate in specific host niches and its susceptibility to host defense mechanisms. We used live imaging to observe the interaction of white and opaque cells with host phagocytic cells. For this purpose, we generated derivatives of the switching-competent strain WO-1 that express green fluorescent protein from a white-specific promoter and red fluorescent protein from an opaque-specific promoter or vice versa. When mixed populations of these differentially labeled white and opaque cells were incubated with human polymorphonuclear neutrophils (PMNs) on a glass slide, the neutrophils selectively phagocytosed and killed white cells, despite frequent physical interaction with opaque cells. White cells were attacked only after they started to form a germ tube, indicating that the suppression of filamentation in opaque cells saved them from recognition by the PMNs. In contrast to neutrophils, dendritic cells internalized white as well as opaque cells. However, when embedded in a collagen matrix, the PMNs also phagocytosed both white and opaque cells with similar efficiency. These results suggest that, depending on the environment, white-opaque switching enablesC. albicansto escape from specific host defense mechanisms.
Role of Pseudomonas aeruginosa Peptidoglycan-Associated Outer Membrane Proteins in Vesicle Formation
Authors: Wessel Aimee K. , Liew Jean , Kwon Taejoon , Marcotte Edward M. , Whiteley Marvin
Published: November 2012

Gram-negative bacteria produce outer membrane vesicles (OMVs) that package and deliver proteins, small molecules, and DNA to prokaryotic and eukaryotic cells. The molecular details of OMV biogenesis have not been fully elucidated, but peptidoglycan-associated outer membrane proteins that tether the outer membrane to the underlying peptidoglycan have been shown to be critical for OMV formation in multiple
Enterobacteriaceae
. In this study, we demonstrate that the peptidoglycan-associated outer membrane proteins OprF and OprI, but not OprL, impact production of OMVs by the opportunistic pathogen
Pseudomonas aeruginosa
. Interestingly, OprF does not appear to be important for tethering the outer membrane to peptidoglycan but instead impacts OMV formation through modulation of the levels of the
Pseudomonas
quinolone signal (PQS), a quorum signal previously shown by our laboratory to be critical for OMV formation. Thus, the mechanism by which OprF impacts OMV formation is distinct from that for other peptidoglycan-associated outer membrane proteins, including OprI.
Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis
Authors: Traag Bjorn A. , Pugliese Antonia , Eisen Jonathan A. , Losick Richard
Published: November 2012

The capacity to form endospores is unique to certain members of the low-G+C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such asClostridiumandBacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors. Mutants of none of the genes exhibited a conspicuous defect in sporulation, but mutants of two,ylxYandylyA, were outcompeted by a wild-type strain under sporulation-inducing conditions, but not during growth. In contrast, aylmCmutant displayed a slight competitive advantage over the wild type specific to sporulation-inducing conditions. The phenotype of aylyAmutant was ascribed to a defect in spore germination efficiency. This work demonstrates the power of combining phylogenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a conserved developmental process.
The Bacillus subtilis Response Regulator Gene
degU
Is Positively Regulated by CcpA and by Catabolite-Repressed Synthesis of ClpC
Authors: Ishii Hiroshi , Tanaka Teruo , Ogura Mitsuo
Published: November 2012

In
Bacillus subtilis
, the response regulator DegU and its cognate kinase, DegS, constitute a two-component system that regulates many cellular processes, including exoprotease production and genetic competence. Phosphorylated DegU (DegU-P) activates its own promoter and is degraded by the ClpCP protease. We observed induction of
degU
by glucose in sporulation medium. This was abolished in two mutants: the
ccpA
(catabolite control protein A) and
clpC
disruptants. Transcription of the promoter of the operon containing
clpC
(PclpC) decreased in the presence of glucose, and the disruption of
ccpA
resulted in derepression of PclpC. However, this was not directly mediated by CcpA, because we failed to detect binding of CcpA to PclpC. Glucose decreased the expression of
clpC
, leading to low cellular concentrations of the ClpCP protease. Thus,
degU
is induced through activation of autoregulation by a decrease in ClpCP-dependent proteolysis of DegU-P. An electrophoretic mobility shift assay showed that CcpA bound directly to the
degU
upstream region, indicating that CcpA activates
degU
through binding. The bound region was narrowed down to 27 bases, which contained a
cre
(
c
atabolite-
r
esponsive
e
lement) sequence with a low match to the
cre
consensus sequence. In a footprint analysis, CcpA specifically protected a region containing the
cre
sequence from DNase I digestion. The induction of
degU
by glucose showed complex regulation of the
degU
gene.
2-Nitrobenzoate 2-Nitroreductase (NbaA) Switches Its Substrate Specificity from 2-Nitrobenzoic Acid to 2,4-Dinitrobenzoic Acid under Oxidizing Conditions
Authors: Kim Yong-Hak , Song Woo-Seok , Go Hayoung , Cha Chang-Jun , Lee Cheolju , Yu Myeong-Hee , Lau Peter C. K. , Lee Kangseok
Published: November 2012

2-Nitrobenzoate 2-nitroreductase (NbaA) of
Pseudomonas fluorescens
strain KU-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-NBA) and 2,4-dinitrobenzoic acid (2,4-DNBA) to the 2-hydroxylamine compounds. Sequence comparison reveals that NbaA contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. The truncated mutant Δ65-74 exhibited markedly reduced activity toward 2,4-DNBA, but its 2-NBA reduction activity was unaffected; however, both activities were abolished in the Δ193-216 mutant, suggesting that these regions are necessary for the catalysis and specificity of NbaA. NbaA showed different lag times for the reduction of 2-NBA and 2,4-DNBA with NADPH, and the reduction of 2,4-DNBA, but not 2-NBA, failed in the presence of 1 mM dithiothreitol or under anaerobic conditions, indicating oxidative modification of the enzyme for 2,4-DNBA. The enzyme was irreversibly inhibited by 5,5′-dithio-
bis
-(2-nitrobenzoic acid) and ZnCl
2
, which bind to reactive thiol/thiolate groups, and was eventually inactivated during the formation of higher-order oligomers at high pH, high temperature, or in the presence of H
2
O
2
. SDS-PAGE and mass spectrometry revealed the formation of intermolecular disulfide bonds by involvement of the two cysteines at positions 141 and 194. Site-directed mutagenesis indicated that the cysteines at positions 39, 103, 141, and 194 played a role in changing the enzyme activity and specificity toward 2-NBA and 2,4-DNBA. This study suggests that oxidative modifications of NbaA are responsible for the differential specificity for the two substrates and further enzyme inactivation through the formation of disulfide bonds under oxidizing conditions.
Paediatric palliative care: intravenous methylnaltrexone relieves constipation
Authors: Yeomanson Daniel , Chohan Osman , Mayer Anton
Published: November 2012

Methylnaltrexone, a peripheral opioid μ-receptor antagonist is licensed for subcutaneous administration for the treatment of severe opioid-induced constipation in adults. We describe the use of intravenous methylnaltrexone in a 3-year-old boy receiving a subcutaneous diamorphine infusion for palliation from widely metastatic alveolar rhabdomyosarcoma. The patient, who had not opened his bowels for 3 weeks despite use of regular conventional laxatives, was given a 150 mcg/kg dose via indwelling central venous catheter. Constipation was relieved within minutes of the injection. There were no side effects noted during or following injection, and no clinically apparent reduction in analgesia. Intravenous methylnaltrexone may provide a valuable additional treatment option in paediatric palliative care, especially for those with an oncological diagnosis, the majority of whom will have indwelling central venous access devices.
Risk of contrast-induced nephropathy in patients undergoing endovascular treatment of acute ischemic stroke
Authors: Sharma Jitendra , Nanda Ashish , Jung Richard S , Mehta Sonal , Pooria Javad , Hsu Daniel P
Published: November 2012

Background and purpose

We report the incidence and risk factors for contrast-induced nephropathy after the use of iodinated contrast for endovascular treatment of acute ischemic stroke.

Methods

A retrospective chart review was performed in 194 consecutive patients who underwent endovascular treatment for acute ischemic stroke between January 2006 and January 2011. No patients were excluded from treatment for elevated creatinine (Cr). Each patient received approximately 150 ml intra-arterial non-ionic low-osmolar contrast agent (Optiray 320) during the endovascular procedure. Contrast-induced nephropathy (CIN) was defined according to the Acute Kidney Injury Network criteria as a relative increase of serum Cr 50% above the baseline or an absolute increase of 0.3 mg/dl at 48 h following the endovascular procedure.

Results

Of 194 patients (mean age 65±14 years), 52% were women (n=100) and 25% (n=48) were diabetic. Baseline Cr levels for 191 patients ranged between 0.4 and 2.7 mg/dl. Three patients on chronic hemodialysis had baseline Cr levels ranging between 5.3 and 6.1 mg/dl. Cr was ≤1.5 mg/dl in 163 patients (84%) and ≥ 1.5 mg/dl in 31 (16%). Three of the 191 patients (1.5%) developed CIN as noted from Cr measurements between baseline and within 48 h. One patient who developed an elevated Cr level had a known history of chronic renal insufficiency (Cr > 1.5 mg/dl) and two had baseline Cr levels within the normal range. An additional CT angiogram was obtained in 44 patients, none of which developed CIN. Female gender and diabetes were not associated with a higher risk of developing CIN.

Conclusions

The risk of developing CIN is low among patients with acute stroke who undergo emergency endovascular treatment. Treatment of acute stroke should be performed irrespective of Cr levels.
Transfemoral endovascular treatment of atherosclerotic stenotic lesions of the left common carotid artery ostium: case series and review of the literature
Authors: Dumont Travis M , Eller Jorge L , Mokin Maxim , Snyder Kenneth V , Hopkins L Nelson , Levy Elad I , Siddiqui Adnan H
Published: November 2012

Objective

Endovascular treatment of atherosclerotic stenosis of the left common carotid artery ostium (LCCAO) represents a technical challenge. Unlike stenting of other supra-aortic trunk lesions, LCCAO stenting is not able to be performed from a retrograde approach through the brachial artery. Stenting may be performed via a retrograde approach with a carotid artery cut-down or with total endovascular technique via a transfemoral approach. A consecutive case series is presented to demonstrate the feasibility and safety of the endovascular transfemoral LCCAO stenting technique.

Methods

Our prospectively maintained database of elective neuroendovascular procedures was searched for cases of LCCAO angioplasty and stenting for atherosclerotic stenosis performed between January 2003 and April 2012. Cases identified were isolated and analyzed for clinical and anatomic data. The primary outcome of interest was the incidence of periprocedural (30-day) neurological or cardiopulmonary complications.

Results

Fourteen patients were treated with a transfemoral approach (mean arterial stenosis 72%; symptomatic lesions 86%). Six (43%) had tandem stenosis of the proximal left internal carotid artery. In these cases, embolic protection was used. Stent revascularization was a technical success in all 14 patients, resulting in <20% residual stenosis in each. One intraprocedural complication (transient ischemic attack) was noted in a patient with symptomatic stenosis. One additional patient was identified who was treated with retrograde stenting due to bilateral leg amputations and no femoral access, with no periprocedural complication.

Conclusions

In our experience, transfemoral stenting of stenotic LCCAO lesions is feasible and no permanent neurological or cardiopulmonary sequelae occurred in 14 patients treated with this technique.
Synthesis, characterization, and bioactivities of platinum(II) complexes bearing pyridinecarboxaldimines containing aliphatic groups
Authors: Stewart Erin L. , Patterson Alyssa E. , O'Neill Taryn , Li Haoxin , Flewelling Andrew , Vogels Christopher M. , Decken Andreas , Lloyd Vett K. , Gray Christopher A. , Westcott Stephen A.
Published: November 2012

Condensation of 2-pyridinecarboxaldehyde with six primary amines containing aliphatic groups gave the corresponding pyridinecarboxaldimines (N-N′R). Addition of these ligands to [PtCl2(coe)]2 (coe = cis-cyclooctene) gave complexes of the type cis-PtCl2(N-N′R) (1: R = propyl, 2: R = hexyl, 3: R = octyl, 4: R = nonyl, 5: R = hexadecyl, and 6: R = octadecyl) in moderate yields. The molecular structure of the hexyl derivative (2) has been confirmed by an X-ray diffraction study. Crystals of 2 were triclinic with a = 8.6858(19) Å, b = 8.7567(19) Å, c = 9.5080(19) Å, α = 76.546(3)°, β = 87.151(3)°, and γ = 78.586(3)° in the space group P1. All platinum complexes show considerable anti-bacterial and anti-mycobacterial properties.
MODELING MOVING BOUNDARY IN SHALLOW WATER BY LBM
Authors: PENG Y. , ZHOU J. G. , ZHANG J. M. , BURROWS R.
Published: November 2012

A lattice Boltzmann model (LBM) for a moving body in shallow waters is developed. Three different schemes, FH's, Guo's and MMP's schemes, for a curved boundary condition at second-order accuracy are used in the study and compared in detail. The multiple-relaxation-time (MRT) is adopted for better stability. In order to deal with the moving body boundary, a certain momentum is added to reflect the interaction between the fluid and the solid; and a refill method for new wetted nodes moving out from solid nodes has been proposed. The described method is applied to simulate static and moving cylinders in shallow waters. The corresponding experiments are further performed for validation of the present model. It is found that all of the three schemes produce similar results that agree well with the experimental data for the static cylinder. However, for the moving boundary, MMP's scheme performs best. Overall, the proposed modeling approach is able to simulate both, static and moving cylinders in shallow water flows at acceptable accuracy.
GLOBAL CONVERGENCE OF TWO KINDS OF THREE-TERM CONJUGATE GRADIENT METHODS WITHOUT LINE SEARCH
Authors: YIN LIANG , CHEN XIONGDA
Published: November 2012

The conjugate gradient method is widely used in unconstrained optimization, especially for large-scale problems. Recently, Zhang et al. proposed a three-term PRP method (TTPRP) and a three-term HS method (TTHS), both of which can produce sufficient descent conditions. In this paper, the global convergence of the TTPRP and TTHS methods is studied, in which the line search procedure is replaced by a fixed formula of stepsize. This character is of significance when the line search is expensive in some particular applications. In addition, relevant computational results are also presented.
THE EFFECTS OF REFLECTIVE SCATTERING IN THE SPIN CORRELATION PARAMETER IN TOP-QUARK PRODUCTION AT THE LHC
Authors: TROSHIN S. M. , TYURIN N. E.
Published: November 2012

The specific effects of the reflective scattering (anti-shadowing) related to the spin correlations in the top-quark production at the LHC are considered. Account for those effects is important in the searches for the signatures of the extra dimensions. It is shown that significant spin correlations could arise at the LHC energies due to reflective scattering and those can affect the signals of the extra dimensions.
INVARIANT FORMULATION OF THE FUNCTIONAL RENORMALIZATION GROUP METHOD FOR U(n)×U(n) SYMMETRIC MATRIX MODELS
Authors: PATKÓS A.
Published: November 2012

The Local Potential Approximation (LPA) to the Wetterich-equation is formulated explicitly in terms of operators, which are invariant under the U (n)× U (n) symmetry group. Complete formulas are presented for the two-flavor ( U (2)× U (2)) case. The same approach leads to a unique natural truncation of the functional driving the renormalization flow of the potential of the three-flavor case ( U (3)× U (3)). The procedure applied to the SU (3)× SU (3) symmetric theory, results in an equation, which potentially allows an RG-investigation of the effect of the 't Hooft term representing the U A(1) anomaly, disentangled from the other operators.
THE EVOLUTION PROPERTIES OF EVEN–EVEN 100-110Pd NUCLEI
Authors: AHMED I. M. , ABDULLAH HEWA Y. , AHMAD S. T. , HOSSAIN I. , KASMIN M. K. , SAEED M. A. , IBRAHIM N.
Published: November 2012

The properties of the yrast states for 100-110 Pd even–even (e–e) nuclei have been established. The relation between the moment of inertia 2ϑ/ℏ2 and the square of the rotational energy (ℏω)2 has been drawn to identify the back-bending that may occur at a certain state for each isotope. The relation between gamma-energy over spin Eγ/I as a function of spin I has been drawn to determine the evolution in each isotope ranging from vibration to rotational properties. The suitable limit in the interacting boson model IBM-1 has been used to calculate the yrast states for each isotope, which are then compared with the experimental results.
THEORETICAL STUDY OF THE STRUCTURES AND PROPERTIES OF (Cl2AlN3)n(n = 2–4) CLUSTERS
Authors: XIA QIYING , MA DENGXUE , ZHAO WENWEI
Published: November 2012

Density functional theory has been employed to study the molecular geometries, energies, infrared vibrational spectra, and thermodynamic properties of the clusters ( Cl2AlN3 )n(n = 1–4) at the B3LYP/6-311+G* level. The optimized clusters ( Cl2AlN3 )n(n = 2–4) all possess cyclic structures formed by Al atoms bridged by the α-nitrogen of the azide groups, and azido in azides has linear structure. The relationships between geometrical parameters and oligomerization degree n are discussed. The gas-phase structures of the trimers prefer to exist in boat-twisting conformation. As for the tetramer, the S4 symmetry structure is the most stable. The infrared spectra are obtained and assigned by vibrational analysis. Trends in thermodynamic properties with temperature and oligomerization degree n are discussed, respectively. A study of their thermodynamic properties suggests that monomer 1A forms clusters (2A, 3A and 3B) can occur spontaneously in the gas phase at temperatures up to 800 K. However, monomer 1A forms tetramers can occur spontaneously at temperatures below 600 K.
MAP kinase kinase kinase-2 (MEKK2) regulates hypertrophic remodeling of the right ventricle in hypoxia-induced pulmonary hypertension
Authors: Brown R. Dale , Ambler S. Kelly , Li Min , Sullivan Timothy M. , Henry Lauren N. , Crossno Joseph T. , Long Carlin S. , Garrington Timothy P. , Stenmark Kurt R.
Published: November 2012

Pulmonary hypertension (PH) results in pressure overload of the right ventricle (RV) of the heart, initiating pathological RV remodeling and ultimately leading to right heart failure. Substantial research indicates that signaling through the MAPK superfamily mediates pathological cardiac remodeling. These considerations led us to test the hypothesis that the regulatory protein MAPKKK-2 (MEKK2) contributes to RV hypertrophy in hypoxia-induced PH. Transgenic mice with global knockout of MEKK2 (MEKK2−/−mice) and age-matched wild-type (WT) mice were exposed to chronic hypobaric hypoxia (10% O2, 6 wk) and compared with animals under normoxia. Exposure to chronic hypoxia induced PH in WT and MEKK2−/−mice. In response to PH, WT mice showed RV hypertrophy, demonstrated as increased ratio of RV weight to body weight, increased RV wall thickness at diastole, and increased cardiac myocyte size compared with normoxic control animals. In contrast, each of these measures of RV hypertrophy seen in WT mice after chronic hypoxia was attenuated in MEKK2−/−mice. Furthermore, chronic hypoxia elicited altered programs of hypertrophic and inflammatory gene expression consistent with pathological RV remodeling in WT mice; MEKK2 deletion selectively inhibited inflammatory gene expression compared with WT mice. The actions of MEKK2 were mediated in part through regulation of the abundance and phosphorylation of its effector, ERK5. In conclusion, signaling by MEKK2 contributes to RV hypertrophy and altered myocardial inflammatory gene expression in response to hypoxia-induced PH. Therapies targeting MEKK2 may protect the myocardium from hypertrophy and pathological remodeling in human PH.
Relaxant effect of all-trans-retinoic acid via NO-sGC-cGMP pathway and calcium-activated potassium channels in rat mesenteric artery
Authors: Wang Yusheng , Han Yu , Yang Jian , Wang Zhen , Liu Li , Wang Wei , Zhou Lin , Wang Dan , Tan Xuerui , Fu Chunjiang , Jose Pedro A. , Zeng Chunyu
Published: November 2012

Intraperitoneal injection of all- trans-retinoic acid (ATRA) results in a reduction of blood pressure in spontaneously hypertensive rats. However, the mechanisms involved in this effect are not clear. We hypothesized that ATRA may relax resistance arteries. In this study, we found that ATRA relaxed phenylephrine-preconstricted mesenteric arterial rings, which were abrogated by the removal of the endothelium. Pretreatment of endothelium-intact arterial rings with an inhibitor of endothelial nitric oxide (NO) synthase, NG-nitro-l-arginine methyl ester (l-NAME), or soluble guanylyl cyclase, 1H-[1,2,4]-oxadiazole-[4,3-α]-quinoxaline-1-one, reduced the vasorelaxant effect of ATRA. Incubation of mesenteric arterial rings with ATRA increased the production of NO and cGMP, which were blocked by NG-nitro-l-arginine methyl ester. The vasorelaxant effect of ATRA was markedly attenuated in the presence of an inhibitor of big conductance calcium-activated potassium channels (charybdotoxin), but not with an inhibitor of voltage-dependent potassium channel (4-aminopyridine) or ATP-sensitive potassium channel (glibenclamide). Activation of retinoic acid receptors (RARs) with CH55 or retinoic X receptors (RXRs) with LGD1069 induced the vasorelaxation of phenylephrine-preconstricted mesenteric arterial rings. The RAR (BMS493) and RXR (UVI3003) antagonists blocked the ATRA-induced vasorelaxation. The vasorelaxant effect ATRA is physiologically relevant because the intravenous infusion of ATRA decreased blood pressure in normotensive rats. We conclude that ATRA relaxes resistance vessels via both RARs and RXRs receptors that are mediated by the endothelium-dependent NO-cGMP pathway, which may participate in the control of blood pressure.
Vascular dysfunction in young, mid-aged and aged mice with latent cytomegalovirus infections
Authors: Gombos R. B. , Brown J. C. , Teefy J. , Gibeault R. L. , Conn K. L. , Schang L. M. , Hemmings D. G.
Published: November 2012

Human cytomegalovirus (HCMV) is associated with vascular diseases in both immunosuppressed and immunocompetent individuals. CMV infections cycle between active and latent phases throughout life. We and others have shown vascular dysfunction during active mouse CMV (mCMV) infections. Few studies have examined changes in physiology during latent CMV infections, particularly vascular responses or whether the negative effects of aging on vascular function and fertility will be exacerbated under these conditions. We measured vascular responses in intact mesenteric and uterine arteries dissected from young, mid-aged, and aged latently mCMV-infected (mCMV genomes are present but infectious virus is undetectable) and age-matched uninfected mice using a pressure myograph. We tested responses to the α1-adrenergic agonist phenylephrine, the nitric oxide donor sodium nitroprusside, and the endothelium-dependent vasodilator methacholine. In young latently mCMV-infected mice, vasoconstriction was increased and vasodilation was decreased in mesenteric arteries, whereas both vasoconstriction and vasodilation were increased in uterine arteries compared with those in age-matched uninfected mice. In reproductively active mid-aged latently infected mice, mesenteric arteries showed little change, whereas uterine arteries showed greatly increased vasoconstriction. These vascular effects may have contributed to the decreased reproductive success observed in mid-aged latently mCMV-infected compared with age-matched uninfected mice (16.7 vs. 46.7%, respectively). In aged latently infected mice, vasodilation is increased in mesenteric and uterine arteries likely to compensate for increased vasoconstriction to mediators other than phenylephrine. The novel results of this study show that even when active mCMV infections become undetectable, vascular dysfunction continues and differs with age and artery origin.
Construction of two novel reciprocal conplastic rat strains and characterization of cardiac mitochondria
Authors: Kumarasamy Sivarajan , Gopalakrishnan Kathirvel , Abdul-Majeed Shakila , Partow-Navid Rod , Farms Phyllis , Joe Bina
Published: November 2012

Because of the lack of appropriate animal models, the potentially causal contributions of inherited mitochondrial genomic factors to complex traits are less well studied compared with inherited nuclear genomic factors. We previously detected variations between the mitochondrial DNA (mtDNA) of the Dahl salt-sensitive (S) rat and the spontaneously hypertensive rat (SHR). Specifically, multiple variations were detected in mitochondrial genes coding for subunits of proteins essential for electron transport, in mitochondrial reactive oxygen species production, and within the D-loop region. To evaluate the effects of these mtDNA variations in the absence of the corresponding nuclear genomic factors as confounding variables, novel reciprocal strains of S and SHR were constructed and characterized. When compared with that of the S rat, the heart tissue from the S.SHRmt conplastic strain wherein the mtDNA of the S rat was substituted with that of the SHR had a significant increase in mtDNA copy number and decrease in mitochondrial reactive oxygen species production. A corresponding increase in aerobic treadmill running capacity and a significant increase in survival that was not related to changes in blood pressure were observed in the S.SHRmt rats compared with the S rat. The reciprocal SHR.Smt rats did not differ from the SHR in any phenotype tested, suggesting lower penetrance of the S mtDNA on the nuclear genomic background of the SHR. These novel conplastic strains serve as invaluable tools to further dissect the relationship between heart function, aerobic fitness, cardiovascular disease progression, and mortality.
IL-13 receptor α2-arginase 2 pathway mediates IL-13-induced pulmonary hypertension
Authors: Cho Won-Kyung , Lee Chang-Min , Kang Min-Jong , Huang Yan , Giordano Frank J. , Lee Patty J. , Trow Terence K. , Homer Robert J. , Sessa William C. , Elias Jack A. , Lee Chun Geun
Published: November 2012

Although previous literature suggests that interleukin (IL)-13, a T-helper type 2 cell effector cytokine, might be involved in the pathogenesis of pulmonary hypertension (PH), direct proof is lacking. Furthermore, a potential mechanism underlying IL-13-induced PH has never been explored. This study's goal was to investigate the role and mechanism of IL-13 in the pathogenesis of PH. Lung-specific IL-13-overexpressing transgenic (Tg) mice were examined for hemodynamic changes and pulmonary vascular remodeling. IL-13 Tg mice spontaneously developed PH phenotype by the age of 2 mo with increased expression and activity of arginase 2 (Arg2). The role of Arg2 in the development of IL-13-stimulated PH was further investigated using Arg2 and IL-13 receptor α2 (Rα2) null mutant mice and the small-interfering RNA (siRNA)-silencing approach in vivo and in vitro, respectively. IL-13-stimulated medial thickening of pulmonary arteries and right ventricle systolic pressure were significantly decreased in the IL-13 Tg mice with Arg2 null mutation. On the other hand, the production of nitric oxide was further increased in the lungs of these mice. In our in vitro evaluations, the recombinant IL-13 treatment significantly enhanced the proliferation of human pulmonary artery smooth muscle cells in an Arg2-dependent manner. The IL-13-stimulated cellular proliferation and the expression of Arg2 in hpaSMC were markedly decreased with IL-13Rα2 siRNA silencing. Our studies demonstrate that IL-13 contributes to the development of PH via an IL-13Rα2-Arg2-dependent pathway. The intervention of this pathway could be a potential therapeutic target in pulmonary arterial hypertension.
The Transmission Disequilibrium/Heterogeneity Test with Parental-Genotype Reconstruction for Refined Genetic Mapping of Complex Diseases
Authors: Han Jing , Shao Yongzhao
Published: November 2012

In linkage analysis for mapping genetic diseases, the transmission/disequilibrium test (TDT) uses the linkage disequilibrium (LD) between some marker and trait loci for precise genetic mapping while avoiding confounding due to population stratification. The sib-TDT (S-TDT) and combined-TDT (C-TDT) proposed by Spielman and Ewens can combine data from families with and without parental marker genotypes (PMGs). For some families with missing PMG, the reconstruction-combined TDT (RC-TDT) proposed by Knapp may be used to reconstruct missing parental genotypes from the genotypes of their offspring to increase power and to correct for potential bias. In this paper, we propose a further extension of the RC-TDT, called the reconstruction-combined transmission disequilibrium/heterogeneity (RC-TDH) test, to take into account the identical-by-descent (IBD) sharing information in addition to the LD information. It can effectively utilize families with missing or incomplete parental genetic marker information. An application of this proposed method to Genetic Analysis Workshop 14 (GAW14) data sets and extensive simulation studies suggest that this approach may further increase statistical power which is particularly valuable when LD is unknown and/or when some or all PMGs are not available.
A Comparison of Implications in Orthomodular Quantum Logic—Morphological Analysis of Quantum Logic
Authors: Fujio Mitsuhiko
Published: November 2012

Morphological operators are generalized to lattices as adjunction pairs (Serra, 1984; Ronse, 1990; Heijmans and Ronse, 1990; Heijmans, 1994). In particular, morphology for set lattices is applied to analyze logics through Kripke semantics (Bloch, 2002; Fujio and Bloch, 2004; Fujio, 2006). For example, a pair of morphological operators as an adjunction gives rise to a temporalization of normal modal logic (Fujio and Bloch, 2004; Fujio, 2006). Also, constructions of models for intuitionistic logic or linear logics can be described in terms of morphological interior and/or closure operators (Fujio and Bloch, 2004). This shows that morphological analysis can be applied to various non-classical logics. On the other hand, quantum logics are algebraically formalized as orhomodular or modular ortho-complemented lattices (Birkhoff and von Neumann, 1936; Maeda, 1980; Chiara and Giuntini, 2002), and shown to allow Kripke semantics (Chiara and Giuntini, 2002). This suggests the possibility of morphological analysis for quantum logics. In this article, to show an efficiency of morphological analysis for quantum logic, we consider the implication problem in quantum logics (Chiara and Giuntini, 2002). We will give a comparison of the 5 polynomial implication connectives available in quantum logics.
Remission of Cognitive Deficits in Parkinson’s Disease: Recovery from a Nonamnestic Mild Cognitive Impairment or Psychiatric Symptoms Remission?
Authors: de Paula Jonas Jardim , Cintra Marco Túlio Gualberto , Miranda Débora Marques , Bicalho Maria Aparecida Camargos , Moares Edgar Nunes , Malloy-Diniz Leandro Fernandes
Published: November 2012

Mild cognitive impairment is a clinical condition more frequent in patients with Parkinson's disease than in general population. The nonamnestic presentations, usually characterized by executive dysfunction, are most prevalent. We present a case report of a Parkinson’s disease patient diagnosed with nonamnestic mild cognitive impairment that showed complete remission of cognitive symptoms after one year. We discuss the possible causes for the remission, focusing on the treatment of medical conditions such as a major depressive episode and vitamin B12 deficiency, in addition to the change of pharmacological treatment. In a third assessment, cognitive performance remained normal. The case report highlights the importance of controlling clinical comorbidities on the assessment and followup of mild cognitive impairment, especially on Parkinson’s disease.
FDM for Elliptic Equations with Bitsadze‐Samarskii‐Dirichlet Conditions
Authors: Ashyralyev Allaberen , Ozesenli Tetikoglu Fatma Songul
Published: November 2012

A numerical method is proposed for solving nonlocal boundary value problem for the multidimensional elliptic partial differential equation with the Bitsadze‐Samarskii‐Dirichlet condition. The first and second‐orders of accuracy stable difference schemes for the approximate solution of this nonlocal boundary value problem are presented. The stability estimates, coercivity, and almost coercivity inequalities for solution of these schemes are established. The theoretical statements for the solutions of these nonlocal elliptic problems are supported by results of numerical examples.
Bilateral Ovarian Endometriomas Presenting as Nonprogress of Labor: First Case Report in the Literature Is Concomitant Surgical Excision during Cesarean Section Advisable?
Authors: Shekhar Shashank , Sharma Chanderdeep , Somya Vinay , Thusoo Meghna , Raina Nidhi
Published: November 2012

Objective. To report the first case of bilateral ovarian endometriomas, leading to nonprogress of labour, successfully excised during cesarean section.Design. Case report.Setting. Department of Obstetrics & Gynecology of Dr. RPGMC Tanda, Kangra, India.Patients. A primigravida in labour at term gestation.Interventions. Surgical management.Main Outcome Measures. Description and treatment of a pregnant woman with bilateral ovarian endometriomas during cesarean section.Results. Successful excision of ovarian endometriomas and reconstruction of the ovaries during cesarean section.Conclusion. Management of incidentally detected endometriomas during cesarean section should be individualized, taking into account the symptoms, size, bilaterality, and adhesion with adjacent organs.