bluuebunny/crossref_metadata_2025 huggingface dataset:
bHLH Transcription Factors That Facilitate K
+
Uptake During Stomatal Opening Are Repressed by Abscisic Acid Through Phosphorylation
Authors: Takahashi Yohei , Ebisu Yuta , Kinoshita Toshinori , Doi Michio , Okuma Eiji , Murata Yoshiyuki , Shimazaki Ken-ichiro
Published: June 2013

Decreasing the transcription of genes encoding K
+
channels contributes to inhibition of stomatal opening in
Arabidopsis
.
Coordinating Neuronal Development
Authors: Gough Nancy R.
Published: June 2013

Brain stem neurons direct the specification of their spinal cord targets, the motor neurons.
Specifying Substrate Specificity
Authors: Wong Wei
Published: June 2013

Distinct intracellular signaling pathways acting on the substrates of a protease could determine which substrates are cleaved.
WHO Group 5 Drugs and Difficult Multidrug-Resistant Tuberculosis: a Systematic Review with Cohort Analysis and Meta-Analysis
Authors: Chang Kwok-Chiu , Yew Wing-Wai , Tam Cheuk-Ming , Leung Chi-Chiu
Published: June 2013

It is often necessary to include WHO group 5 drugs in the treatment of extensively drug-resistant tuberculosis (XDR-TB) and fluoroquinolone-resistant multidrug-resistant tuberculosis (MDR-TB). As clinical evidence about the use of group 5 drugs is scarce, we conducted a systematic review using published individual patient data. We searched PubMed and OvidSP through 7 April 2013 for publications in English to assemble a cohort with fluoroquinolone-resistant MDR-TB treated with group 5 drugs. Favorable outcome was defined as sputum culture conversion, cure, or treatment completion in the absence of death, default, treatment failure, or relapse. A cohort of 194 patients was assembled from 20 articles involving 12 geographical regions. In descending order of frequency, linezolid was used in treatment of 162 (84%) patients, macrolides in 84 (43%), clofazimine in 65 (34%), amoxicillin with clavulanate in 56 (29%), thioridazine in 18 (9%), carbapenem in 16 (8%), and high-dose isoniazid in 16 (8%). Cohort analysis with robust Poisson regression models and random-effects meta-analysis similarly suggested that linezolid use significantly increased the probability (95% confidence interval) of favorable outcome by 57% (10% to 124%) and 55% (10% to 121%), respectively. Defining significant associations by risk ratios ≥ 1.2 or ≤ 0.9, neither cohort analysis nor meta-analysis demonstrated any significant add-on benefit from the use of other group 5 drugs with respect to outcome for patients treated with linezolid, although selection bias might have led to underestimation of their effects. Our findings substantiated the use of linezolid in the treatment of XDR-TB or fluoroquinolone-resistant MDR-TB and call for further studies to evaluate the roles of other group 5 drugs.
Relationship between Ceftolozane-Tazobactam Exposure and Drug Resistance Amplification in a Hollow-Fiber Infection Model
Authors: VanScoy Brian , Mendes Rodrigo E. , Castanheira Mariana , McCauley Jennifer , Bhavnani Sujata M. , Forrest Alan , Jones Ronald N. , Okusanya Olanrewaju O. , Friedrich Lawrence V. , Steenbergen Judith , Ambrose Paul G.
Published: June 2013

In an era of rapidly emerging antimicrobial-resistant bacteria, it is critical to understand the importance of the relationships among drug exposure, duration of therapy, and selection of drug resistance. Herein we describe the results of studies designed to determine the ceftolozane-tazobactam exposure necessary to prevent the amplification of drug-resistant bacterial subpopulations in a hollow-fiber infection model. The challenge isolate was a CTX-M-15-producing
Escherichia coli
isolate genetically engineered to transcribe a moderate level of
bla
CTX-M-15
. This organism's
bla
CTX-M-15
transcription level was confirmed by relative quantitative reverse transcription-PCR (qRT-PCR), β-lactamase hydrolytic assays, and a ceftolozane MIC value of 16 mg/liter. In these studies, the experimental duration (10 days), ceftolozane-tazobactam dose ratio (2:1), and dosing interval (every 8 h) were selected to approximate those expected to be used clinically. The ceftolozane-tazobactam doses studied ranged from 125-62.5 to 1,500-750 mg. Negative- and positive-control arms included no treatment and piperacillin-tazobactam at 4.5 g every 6 h, respectively. An inverted-U-shaped function best described the relationship between bacterial drug resistance amplification and drug exposure. The least- and most-intensive ceftolozane-tazobactam dosing regimens, i.e., 125-62.5, 750-375, 1,000-500, and 1,500-750 mg, did not amplify drug resistance, while drug resistance amplification was observed with intermediate-intensity dosing regimens (250-125 and 500-250 mg). For the intermediate-intensity ceftolozane-tazobactam dosing regimens, the drug-resistant subpopulation became the dominant population by days 4 to 6. The more-intensive ceftolozane-tazobactam dosing regimens (750-375, 1,000-500, and 1,500-750 mg) not only prevented drug resistance amplification but also virtually sterilized the model system. These data support the selection of ceftolozane-tazobactam dosing regimens that minimize the potential for on-therapy drug resistance amplification.
Sublethal Ciprofloxacin Treatment Leads to Rapid Development of High-Level Ciprofloxacin Resistance during Long-Term Experimental Evolution of Pseudomonas aeruginosa
Authors: Jørgensen Karin Meinike , Wassermann Tina , Jensen Peter Østrup , Hengzuang Wang , Molin Søren , Høiby Niels , Ciofu Oana
Published: June 2013

The dynamics of occurrence and the genetic basis of ciprofloxacin resistance were studied in a long-term evolution experiment (940 generations) in wild-type, reference strain (PAO1) and hypermutable (PAOΔmutS and PAOMY-Mgm)
P. aeruginosa
populations continuously exposed to sub-MICs (1/4) of ciprofloxacin. A rapid occurrence of ciprofloxacin-resistant mutants (MIC of ≥12 μg/ml, representing 100 times the MIC of the original population) were observed in all ciprofloxacin-exposed lineages of PAOΔmutS and PAOMY-Mgm populations after 100 and 170 generations, respectively, and in one of the PAO1 lineages after 240 generations. The genetic basis of resistance was mutations in
gyrA
(C248T and G259T) and
gyrB
(C1397A). Cross-resistance to beta-lactam antibiotics was observed in the bacterial populations that evolved during exposure to sublethal concentrations of ciprofloxacin. Our study shows that mutants with high-level ciprofloxacin resistance are selected in
P. aeruginosa
bacterial populations exposed to sub-MICs of ciprofloxacin. This can have implications for the long-term persistence of resistant bacteria and spread of antibiotic resistance by exposure of commensal bacterial flora to low antibiotic concentrations.
Activity of the HIV-1 Attachment Inhibitor BMS-626529, the Active Component of the Prodrug BMS-663068, against CD4-Independent Viruses and HIV-1 Envelopes Resistant to Other Entry Inhibitors
Authors: Li Zhufang , Zhou Nannan , Sun Yongnian , Ray Neelanjana , Lataillade Max , Hanna George J. , Krystal Mark
Published: June 2013

BMS-626529 is a novel small-molecule HIV-1 attachment inhibitor active against both CCR5- and CXCR4-tropic viruses. BMS-626529 functions by preventing gp120 from binding to CD4. A prodrug of this compound, BMS-663068, is currently in clinical development. As a theoretical resistance pathway to BMS-663068 could be the development of a CD4-independent phenotype, we examined the activity of BMS-626529 against CD4-independent viruses and investigated whether resistance to BMS-626529 could be associated with a CD4-independent phenotype. Finally, we evaluated whether cross-resistance exists between BMS-626529 and other HIV-1 entry inhibitors. Two laboratory-derived envelopes with a CD4-independent phenotype (one CXCR4 tropic and one CCR5 tropic), five envelopes from clinical isolates with preexisting BMS-626529 resistance, and several site-specific mutant BMS-626529-resistant envelopes were examined for their dependence on CD4 for infectivity or susceptibility to BMS-626529. Viruses resistant to other entry inhibitors (enfuvirtide, maraviroc, and ibalizumab) were also examined for susceptibility to BMS-626529. Both CD4-independent laboratory isolates retained sensitivity to BMS-626529 in CD4
−
cells, while HIV-1 envelopes from viruses resistant to BMS-626529 exhibited no evidence of a CD4-independent phenotype. BMS-626529 also exhibited inhibitory activity against ibalizumab- and enfuvirtide-resistant envelopes. While there appeared to be some association between maraviroc resistance and reduced susceptibility to BMS-626529, an absolute correlation cannot be presumed, since some CCR5-tropic maraviroc-resistant envelopes remained sensitive to BMS-626529. Clinical use of the prodrug BMS-663068 is unlikely to promote resistance via generation of CD4-independent virus. No cross-resistance between BMS-626529 and other HIV entry inhibitors was observed, which could allow for sequential or concurrent use with different classes of entry inhibitors.
Multicenter Study of High-Dose Daptomycin for Treatment of Enterococcal Infections
Authors: Casapao Anthony M. , Kullar Ravina , Davis Susan L. , Levine Donald P. , Zhao Jing J. , Potoski Brian A. , Goff Debra A. , Crank Christopher W. , Segreti John , Sakoulas George , Cosgrove Sara E. , Rybak Michael J.
Published: June 2013

Enterococci are among the leading pathogens isolated in hospital-acquired infections. Current antimicrobial options for vancomycin-resistant enterococci (VRE) are limited. Prior data suggest that daptomycin at >6 mg/kg of body weight/day may be used to treat enterococcal infections. We retrospectively evaluated the effectiveness and safety of high-dose daptomycin (HD-daptomycin) therapy (>6 mg/kg) in a multicenter cohort of adult patients with enterococcal infections to describe the characteristics and outcomes. Two hundred forty-five patients were evaluated.
Enterococcus faecium
was identified in 175 (71%), followed by
Enterococcus faecalis
in 49 (20%) and
Enterococcus
spp. in 21 (9%); overall, 204 (83%) isolates were VRE. Enterococcal infections included bacteremia (173, 71%) and intra-abdominal (35, 14%) and bone and joint (25, 10%) infections. The median dosage and duration of HD-daptomycin were 8.2 mg/kg/day (interquartile range [IQR], 7.7 to 9.7) and 10 days (IQR, 6 to 15), respectively. The overall clinical success rate was 89% (193/218), and microbiological eradication was observed in 93% (177/191) of patients. The median time to clearance of blood cultures on HD-daptomycin was 3 days (IQR, 2 to 5). The 30-day all-cause mortality rate was 27%, and 5 (2%) patients developed daptomycin-nonsusceptible enterococcal strains while on HD-daptomycin. Seven patients (3%) had creatine phosphokinase (CPK) elevation, yet no HD-daptomycin regimen was discontinued due to an elevated CPK and all patients were asymptomatic. Overall, there was a high frequency of clinical success and microbiological eradication in patients treated with HD-daptomycin for enterococcal infections, even in patients with complicated and difficult-to-treat infections. No adverse event-related discontinuation of HD-daptomycin was noted. HD-daptomycin may be an option for the treatment of enterococcal infections.
Myxomavirus-Derived Serpin Prolongs Survival and Reduces Inflammation and Hemorrhage in an Unrelated Lethal Mouse Viral Infection
Authors: Chen Hao , Zheng Donghang , Abbott Jeff , Liu Liying , Bartee Mee Y. , Long Maureen , Davids Jennifer , Williams Jennifer , Feldmann Heinz , Strong James , Grau Katrina R. , Tibbetts Scott , Macaulay Colin , McFadden Grant , Thoburn Robert , Lomas David A. , Spinale Francis G. , Virgin Herbert W. , Lucas Alexandra
Published: June 2013

Lethal viral infections produce widespread inflammation with vascular leak, clotting, and bleeding (disseminated intravascular coagulation [DIC]), organ failure, and high mortality. Serine proteases in clot-forming (thrombotic) and clot-dissolving (thrombolytic) cascades are activated by an inflammatory cytokine storm and also can induce systemic inflammation with loss of normal
ser
ine
p
rotease
in
hibitor (serpin) regulation. Myxomavirus secretes a potent anti-inflammatory serpin, Serp-1, that inhibits clotting factor X (fX) and thrombolytic tissue- and urokinase-type plasminogen activators (tPA and uPA) with anti-inflammatory activity in multiple animal models. Purified serpin significantly improved survival in a murine gammaherpesvirus 68 (MHV68) infection in gamma interferon receptor (IFN-γR) knockout mice, a model for lethal inflammatory vasculitis. Treatment of MHV68-infected mice with neuroserpin, a mammalian serpin that inhibits only tPA and uPA, was ineffective. Serp-1 reduced virus load, lung hemorrhage, and aortic, lung, and colon inflammation in MHV68-infected mice and also reduced virus load. Neuroserpin suppressed a wide range of immune spleen cell responses after MHV68 infection, while Serp-1 selectively increased CD11c
+
splenocytes (macrophage and dendritic cells) and reduced CD11b
+
tissue macrophages. Serp-1 altered gene expression for coagulation and inflammatory responses, whereas neuroserpin did not. Serp-1 treatment was assessed in a second viral infection, mouse-adapted Zaire ebolavirus in wild-type BALB/c mice, with improved survival and reduced tissue necrosis. In summary, treatment with this unique myxomavirus-derived serpin suppresses systemic serine protease and innate immune responses caused by unrelated lethal viral infections (both RNA and DNA viruses), providing a potential new therapeutic approach for treatment of lethal viral sepsis.
Na
+
/H
+
Antiport Is Essential for Yersinia pestis Virulence
Authors: Minato Yusuke , Ghosh Amit , Faulkner Wyatt J. , Lind Erin J. , Schesser Bartra Sara , Plano Gregory V. , Jarrett Clayton O. , Hinnebusch B. Joseph , Winogrodzki Judith , Dibrov Pavel , Häse Claudia C.
Published: June 2013

Na
+
/H
+
antiporters are ubiquitous membrane proteins that play a central role in the ion homeostasis of cells. In this study, we examined the possible role of Na
+
/H
+
antiport in
Yersinia pestis
virulence and found that
Y. pestis
strains lacking the major Na
+
/H
+
antiporters, NhaA and NhaB, are completely attenuated in an
in vivo
model of plague. The
Y. pestis
derivative strain lacking the
nhaA
and
nhaB
genes showed markedly decreased survival in blood and blood serum
ex vivo
. Complementation of either
nhaA
or
nhaB
in
trans
restored the survival of the
Y. pestis nhaA nhaB
double deletion mutant in blood. The
nhaA nhaB
double deletion mutant also showed inhibited growth in an artificial serum medium, Opti-MEM, and a rich LB-based medium with Na
+
levels and pH values similar to those for blood. Taken together, these data strongly suggest that intact Na
+
/H
+
antiport is indispensable for the survival of
Y. pestis
in the bloodstreams of infected animals and thus might be regarded as a promising noncanonical drug target for infections caused by
Y. pestis
and possibly for those caused by other blood-borne bacterial pathogens.
Identification of Salmonella enterica Serovar Pullorum Antigenic Determinants Expressed
In Vivo
Authors: Li Qiuchun , Hu Yachen , Chen Jing , Liu Zhicheng , Han Jun , Sun Lin , Jiao Xinan
Published: June 2013

Salmonella enterica
serovar Pullorum affecting poultry causes pullorum disease and results in severe economic loss in the poultry industry. Currently, it remains a major threat in countries with poor poultry surveillance and no efficient control measures. As
S
. Pullorum could induce strong humoral immune responses, we applied an immunoscreening technique, the
in vivo
-induced antigen technology (IVIAT), to identify immunogenic bacterial proteins expressed or upregulated during
S
. Pullorum infection. Convalescent-phase sera from chickens infected with
S
. Pullorum were pooled, adsorbed against antigens expressed
in vitro
, and used to screen an
S
. Pullorum genomic expression library. Forty-five proteins were screened out, and their functions were implicated in molecular biosynthesis and degradation, transport, metabolism, regulation, cell wall synthesis and antibiotic resistance, environmental adaptation, or putative functions. In addition, 11 of these 45 genes were assessed for their differential expression by quantitative real-time reverse transcription-PCR (RT-PCR), revealing that 9 of 11 genes were upregulated to different degrees under
in vivo
conditions, especially the regulator of virulence determinants,
phoQ
. Then, four
in vivo
-induced proteins (ShdA, PhoQ, Cse3, and PbpC) were tested for their immunoreactivity in 28 clinical serum samples from chickens infected with
S
. Pullorum. The rate of detection of antibodies against ShdA reached 82% and was the highest among these proteins. ShdA is a host colonization factor known to be upregulated
in vivo
and related to the persistence of
S
. Typhimurium in the intestine. Furthermore, these antigens identified by IVIAT warrant further evaluation for their contributions to pathogenesis, and more potential roles, such as diagnostic, therapeutic, and preventive uses, need to be developed in future studies.
Genetic Analysis of the Role of
yfiR
in the Ability of Escherichia coli CFT073 To Control Cellular Cyclic Dimeric GMP Levels and To Persist in the Urinary Tract
Authors: Raterman Erica L. , Shapiro Daniel D. , Stevens Daniel J. , Schwartz Kevin J. , Welch Rodney A.
Published: June 2013

During urinary tract infections (UTIs), uropathogenic
Escherichia coli
must maintain a delicate balance between sessility and motility to achieve successful infection of both the bladder and kidneys. Previous studies showed that cyclic dimeric GMP (c-di-GMP) levels aid in the control of the transition between motile and nonmotile states in
E. coli
. The
yfiRNB
locus in
E. coli
CFT073 contains genes for YfiN, a diguanylate cyclase, and its activity regulators, YfiR and YfiB. Deletion of
yfiR
yielded a mutant that was attenuated in both the bladder and the kidneys when tested in competition with the wild-type strain in the murine model of UTI. A double
yfiRN
mutant was not attenuated in the mouse model, suggesting that unregulated YfiN activity and likely increased cytoplasmic c-di-GMP levels cause a survival defect. Curli fimbriae and cellulose production were increased in the
yfiR
mutant. Expression of
yhjH
, a gene encoding a proven phosphodiesterase, in CFT073 Δ
yfiR
suppressed the overproduction of curli fimbriae and cellulose and further verified that deletion of
yfiR
results in c-di-GMP accumulation. Additional deletion of
csgD
and
bcsA
, genes necessary for curli fimbriae and cellulose production, respectively, returned colonization levels of the
yfiR
deletion mutant to wild-type levels. Peroxide sensitivity assays and iron acquisition assays displayed no significant differences between the
yfiR
mutant and the wild-type strain. These results indicate that dysregulation of c-di-GMP production results in pleiotropic effects that disable
E. coli
in the urinary tract and implicate the c-di-GMP regulatory system as an important factor in the persistence of uropathogenic
E. coli in vivo
.
Refractory PMR with aortitis: life-saving treatment with anti-IL6 monoclonal antibody (tocilizumab) and surgical reconstruction of the ascending aorta
Authors: Ashraf Fahd Adeeb Mohamed , Anjum Shakeel , Hussaini Abid , Fraser Alexander
Published: June 2013

Aortitis is uncommon but well described in patients with polymyalgia rheumatica (PMR). While glucocorticoid remains the mainstay therapy for large-vessel vasculitis, there have been cases where tocilizumab therapy led to clinical and serological improvement in patients with relapsing or refractory disease. We report a case of life-threatening PMR with aortitis in the absence of manifestations related to giant cell arteritis, which, having failed to respond to corticosteroid therapy, was successfully treated with tocilizumab and emergency reconstruction of the ascending aorta. This case adds to the literature supporting the potential value of interleukin-6 inhibition in rare rheumatological conditions such as inflammatory aortitis.
Atrioventricular accessory pathway with anterograde decremental conduction property
Authors: Fujita Satoshi , Fujii Eitaro , Sugiura Shinya , Ito Masaaki
Published: June 2013

We report a case of atrioventricular (AV) accessory pathway with anterograde decremental conduction property. The δ wave polarity suggested the presence of a right posteroseptal accessory AV pathway. During atrial pacing, Wenckebach-type AV block over the accessory pathway was observed with prolongation of the local AV conduction time without the change in QRS morphology. No retrograde ventriculoatrial conduction was observed. During mapping of the right midseptal area, mechanical conduction block at the level of the proximal input to the accessory pathway was induced repeatedly by catheter manipulation. Radiofrequency energy delivery eliminated the accessory pathway. In this case only the bump phenomenon was the best marker of successful ablation.
Prophylactic decompression of extensor pollicis longus to prevent rupture
Authors: Navaratnam A V , Ball S , Eckersley R
Published: June 2013

We present a case of a patient with spontaneous rupture of right extensor pollicis longus (EPL) tendon, who had also developed left wrist pain and weakness in his left EPL that MRI studies confirmed to be caused by tendinosis. Subsequently, decompression of left EPL and reconstruction of right EPL with palmaris longus tendon graft was undertaken. In this case, decompression of the left EPL tendon led to resolution of the patient's symptoms as well as preventing tendon rupture. We advocate the use of ultrasound imaging to evaluate EPL in these cases and prophylactic decompression of EPL tendon to avoid rupture in those patients found to have tendinosis.
A complementary component to atypical haemolytic uraemic syndrome
Authors: Gandhi Vanita , Burns Aine , Goodship Timothy
Published: June 2013

We describe a case of a 22-year-old man who presented with clinical features of atypical haemolytic uraemic syndrome and in whom genetic analysis of complement regulatory proteins demonstrated a CD46 mutation. He was treated with plasma exchange, intermittent haemodialysis and blood transfusions. At 6-month follow-up his haematological parameters and renal function showed complete resolution, and he experienced no further disease recurrence in the subsequent year.
Republished: Building a culture of safety through team training and engagement
Authors: Thomas Lily , Galla Catherine
Published: June 2013

Medical errors continue to occur despite multiple strategies devised for their prevention. Although many safety initiatives lead to improvement, they are often short lived and unsustainable. Our goal was to build a culture of patient safety within a structure that optimised teamwork and ongoing engagement of the healthcare team. Teamwork impacts the effectiveness of care, patient safety and clinical outcomes, and team training has been identified as a strategy for enhancing teamwork, reducing medical errors and building a culture of safety in healthcare. Therefore, we implemented Team Strategies and Tools to Enhance Performance and Patient Safety (TeamSTEPPS), an evidence-based framework which was used for team training to create transformational and/or incremental changes; facilitating transformation of organisational culture, or solving specific problems. To date, TeamSTEPPS (TS) has been implemented in 14 hospitals, two Long Term Care Facilities, and outpatient areas across the North Shore LIJ Health System. 32 150 members of the healthcare team have been trained. TeamSTEPPS was piloted at a community hospital within the framework of the health system's organisational care delivery model, the Collaborative Care Model to facilitate sustainment. AHRQ's Hospital Survey on Patient Safety Culture, (HSOPSC), was administered before and after implementation of TeamSTEPPS, comparing the perception of patient safety by the heathcare team. Pilot hospital results of HSOPSC show significant improvement from 2007 (pre-TeamSTEPPS) to 2010. System-wide results of HSOPSC show similar trends to those seen in the pilot hospital. Valuable lessons for organisational success from the pilot hospital enabled rapid spread of TeamSTEPPS across the rest of the health system.
Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime
Authors: Forsberg Lars Anders , Absher Devin , Dumanski Jan Piotr
Published: June 2013

The heritability of most common, multifactorial diseases is rather modest and known genetic effects account for a small part of it. The remaining portion of disease aetiology has been conventionally ascribed to environmental effects, with an unknown part being stochastic. This review focuses on recent studies highlighting stochastic events of potentially great importance in human disease—the accumulation of post-zygotic structural aberrations with age in phenotypically normal humans. These findings are in agreement with a substantial mutational load predicted to occur during lifetime within the human soma. A major consequence of these results is that the genetic profile of a single tissue collected at one time point should be used with caution as a faithful portrait of other tissues from the same subject or the same tissue throughout life. Thus, the design of studies in human genetics interrogating a single sample per subject or applying lymphoblastoid cell lines may come into question. Sporadic disorders are common in medicine. We wish to stress the non-heritable genetic variation as a potentially important factor behind the development of sporadic diseases. Moreover, associations between post-zygotic mutations, clonal cell expansions and their relation to cancer predisposition are central in this context. Post-zygotic mutations are amenable to robust examination and are likely to explain a sizable part of non-heritable disease causality, which has routinely been thought of as synonymous with environmental factors. In view of the widespread accumulation of genetic aberrations with age and strong predictions of disease risk from such analyses, studies of post-zygotic mutations may be a fruitful approach for delineation of variants that are causative for common human disorders.
Appetite sensations and substrate metabolism at rest, during exercise, and recovery: impact of a high-calcium meal
Authors: Gonzalez Javier T. , Rumbold Penny L.S. , Stevenson Emma J.
Published: June 2013

The aim of this study was to investigate the effects of the calcium content of a high-carbohydrate, pre-exercise meal on substrate metabolism and appetite sensations before, during, and after exercise. Nine active males participated in 2 trials in a double-blind, randomised, crossover design. After consuming a high carbohydrate (1.5 g·kg−1 of body mass) breakfast with a calcium content of either 3 (control trial) or 9 mg·kg−1 of body mass (high milk-calcium (CAL)), participants ran at 60% peak oxygen uptake for 60 min. Following exercise, a recovery drink was consumed and responses were investigated for a further 90 min. Blood and expired gas were sampled throughout to determine circulating substrate and hormone concentrations and rates of substrate oxidation. Visual analogue scales were also administered to determine subjective appetite sensations. Neither whole-body lipid oxidation nor non-esterified fatty acid availability differed between trials. The area under the curve for the first hour following breakfast consumption was 16% (95% confidence interval: 0%–35%) greater for fullness and 10% (95% confidence interval: 2%–19%) greater for insulin in the CAL trial but these differences were transient and not apparent later in the trial. This study demonstrates that increasing the calcium content of a high carbohydrate meal transiently increases insulinemia and fullness but substrate metabolism is unaffected.
Potato MYB and bHLH transcription factors associated with anthocyanin intensity and common scab resistance
Authors: Tai Helen H. , Goyer Claudia , Murphy Agnes M.
Published: June 2013

MYB and bHLH are large transcription factor families with largely uncharacterized biological functions. The patterns of expression of 42 MYB and 58 bHLH transcription factor genes were examined in potato clones that were demonstrated to have variation in anthocyanin intensity and common scab resistance to assess their possible involvement in regulating these traits. The control of expression of biosynthetic enzymes in regulation of anthocyanin intensity was also evaluated. The dihydroflavonol 4-reductase (DFR) gene, a key enzyme in the pathway, had the highest correlation with gene expression and anthocyanin intensity (quantified as levels of anthocyanidins). Expression of five uncharacterized MYB and three bHLH genes was also highly correlated with anthocyanin intensity, suggesting that they could be regulators of biosynthetic enzyme gene expression. The same potato clones were also demonstrated to have variation in resistance to Streptomyces scabiei, the causal pathogen of common scab in potato. Correlation analysis was used to show that anthocyanin intensity was not associated with common scab resistance. However, common scab resistance was correlated with expression of another two MYB and three bHLH genes, indicating that they might be involved in the regulation of the defense response of potato against the common scab pathogen.
A simple variance estimator for the trapezoidal area-under-the-curve estimator of the spawner abundance of Pacific salmon
Authors: Millar Russell B. , Jordan Chris E.
Published: June 2013

The trapezoidal area-under-the-curve (TAUC) method is the simplest and most widely used method for estimating the spawning abundance of Pacific salmon from periodic surveys of spawner counts within a surveyed area. However, there is currently no method to estimate the precision of the estimated spawner abundance from the survey data. For this reason the Gaussian area-under-the-curve (GAUC) method was recently presented as an easily implemented alternative that has the advantage of having a variance estimator. However, under a diverse variety of simulation scenarios, the TAUC estimator was seen to be a slightly better estimator of escapement on the basis of mean squared error. It is shown here that a variance estimator for the TAUC method can be obtained as an immediate by-product of the GAUC method. Furthermore, this new approach can easily be extended to accommodate asymmetric and multimodal patterns of spawner abundance by the use of basis splines.
Chemical transformations in downed logs and snags of mixed boreal species during decomposition
Authors: Strukelj Manuella , Brais Suzanne , Quideau Sylvie A. , Angers Virginie A. , Kebli Hedi , Drapeau Pierre , Oh Se-Woung
Published: June 2013

Snags and downed logs are substantial components of the detrital carbon pool in boreal forests. Effects of their decomposition on chemical and physical characteristics of the forest floor remain relatively unknown. The main objective of this study was to characterize chemical transformations of decaying logs and snags of common tree species in the boreal mixedwood forest. Logs and snags from a wide range of decay classes were sampled and analyzed by solid-state 13C nuclear magnetic resonance spectroscopy and by near-infrared spectroscopy. Little or moderate chemical changes appeared in fresh and moderately decayed snags and logs, but in well-decayed logs, substantial degradation of carbohydrates and increases in lignin concentrations occurred. Deciduous species had initially more carbohydrates than coniferous species, but decomposition narrowed their differences, and in well-decayed logs, species differed mainly in terms of their lignin concentrations. Well-decayed deciduous logs reached very low wood densities, and their integration into the forest floor and long-term preservation remains questionable. In contrast, chemical composition of well-decayed coniferous logs resembles that of lignic forest floor (i.e., forest floor originating from deadwood decomposition), with preserved lignins, carbohydrates, and alkyl carbon compounds. Decomposed coniferous wood thus contributes to chemical heterogeneity of the forest floor, possibly promoting diversity of decomposers as well as carbon retention in soils.
Role of Rho-GTPases and their regulatory proteins in glomerular podocyte function
Authors: Mouawad Flaviana , Tsui Harmony , Takano Tomoko
Published: June 2013

Podocytes play a critical role in maintaining glomerular permselectivity. It has been long recognized that their intricate actin-based structures are tightly associated with their normal function; however, the precise mechanisms by which podocytes form and maintain their complex structure had been poorly understood until the intensive investigations on podocyte biology began in 1998, triggered by the breakthrough discovery of nephrin. This review summarizes the recent discoveries of the molecular mechanisms by which the actin cytoskeleton is regulated in podocytes. A particular focus will be on the role of the Rho-family of small GTPases, represented by RhoA, Rac1, and Cdc42. Rho-GTPases are known for their versatile cellular functions, most importantly for the actin regulatory roles. We will also discuss the potential roles of the 3 groups of proteins known to regulate Rho-GTPases, namely GTPase-activating proteins, guanine nucleotide exchange factors, and guanine nucleotide dissociation inhibitors.
Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data
Authors: Lamara Mebarek , Zhang Li Yi , Marchand Suzanne , Tinker Nicholas A. , Belzile François
Published: June 2013

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged from 0.34 to 0.86 ([Formula: see text] = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 ([Formula: see text] = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (P < 0.001) r2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.
RADIATION STUDIES FOR THE Mu2e EXPERIMENT: A REVIEW
Authors: PRONSKIKH V. S.
Published: June 2013

The Mu2e experiment being designed at Fermilab will be searching for a rare event — conversion of muon into electron in the field of a nucleus without emission of neutrinos — observation of which would provide unambiguous evidence for physics beyond the Standard Model, making use of an 8 GeV 8 kW proton beam. As an experiment to be performed at the Intensity Frontier, taking advantage of high-intensity proton beams, the Mu2e experimental setup will be residing in a harsh radiation environment created by secondary particle fluxes.

Radiation quantities in different parts of the Mu2e apparatus, such as neutron flux, peak power density, displacements per atom (DPA), absorbed dose, dynamic heat load simulated using the MARS15 code are reviewed in this work. Radiation levels and requirements for Heat and Radiation Shield (HRS), Transport Solenoid (TS), residual dose and decay heat from the Mu2e target, beam dump design, rates in Cosmic Ray Veto (CRV) counters as well as stopping target monitor (STM) are considered. Airflow, surface and ground water activation are estimated. Recent developments in the MARS15 DPA model applied in this work are described, their consequences are discussed.
DARK ENERGY FROM A POSITIVE JERK PARAMETER
Authors: LUONGO ORLANDO
Published: June 2013

In this paper, we demonstrate that the variation of acceleration, namely the jerk parameter j, could give hints for determining the dark energy equation of state (EoS). In particular, it is possible to show that a viable cosmological model is compatible with a constant jerk, here conventionally rewritten as j = 1+ϵ, with ϵ > 0 representing a departure from the ΛCDM model. This suggests that the cosmological constant could be seen as a limiting case of a more general dark energy model. We use the most recent union 2.1 compilation of supernovae Ia, showing at 1σ confidence level, that j is compatible with the condition j ≥ 1. In doing so, we infer a corresponding cosmological model, viable with a negative acceleration parameter, in the observed range -1 < q0 < 0.
SU(5/3) SUPERALGEBRA AND ITS REPRESENTATIONS OF FUNDAMENTAL PARTICLES
Authors: KIM CHANG-HO , KIM SEUNG KOOK , PARK YOUNG-JAI
Published: June 2013

We study the lowest-dimensional typical and atypical representations of SU(5/3) superalgebra as a possible unified gauge theory having a natural SU(5) subalgebra with SU(3) extra structure, which will be used to accommodate three generations of fundamental particles. By using Kac–Dynkin weight techniques, we find that all known quarks and leptons can be really accommodated in one atypical irreducible representation (irrep) of SU(5/3).
TOWARD A PROOF OF LONG RANGE ORDER IN 4D SU(N) LATTICE GAUGE THEORY
Authors: GRADY MICHAEL
Published: June 2013

An extended version of four-dimensional (4D) SU(2) lattice gauge theory is considered in which different inverse coupling parameters are used, [Formula: see text] for plaquettes which are purely space-like, and βV for those which involve the Euclidean time-like direction. It is shown that when βH = ∞ the partition function becomes, in the Coulomb gauge, exactly that of a set of non-interacting three-dimensional (3D) O(4) classical Heisenberg models. Long range order (LRO) at low temperatures (weak coupling) has been rigorously proven for this model. It is shown that the correlation function demonstrating spontaneous magnetization in the ferromagnetic phase is a continuous function of gH at gH = 0 and therefore, that the spontaneously broken phase enters the (βH, βV) phase plane (no step discontinuity at the edge). Once the phase transition line has entered, it can only exit at another identified edge, which requires the SU(2) gauge theory within also to have a phase transition at finite β. A phase exhibiting spontaneous breaking of the remnant symmetry left after Coulomb gauge fixing, the relevant symmetry here, is non-confining. Easy extension to the SU (N) case implies that the continuum limit of zero-temperature 4D SU (N) lattice gauge theories is not confining, in other words, gluons by themselves do not produce a confinement.
A MNA-BASED UNIFIED IDEAL SWITCH MODEL FOR ANALYSIS OF SWITCHING CIRCUITS
Authors: YILDIZ ALI BEKIR
Published: June 2013

The paper proposes a unified switch model for the analysis of circuits with ideal switches. The model is unique and valid for all states of switches. The developed model is based on modified nodal analysis (MNA) that exploits an efficient algorithm developed for linear active circuits. The analysis with the new switch model requires only one topology and uses the uniform system equations regardless of states of switches. The system equations and the states of switches are updated by control variables, used in the model. There are no restrictions on circuit topology and switch connections. The switches can be both externally and internally controlled. The inconsistent initial value problem and Dirac delta impulses occurring because of ideal switch are discussed in detail. Two examples are given concerning the analysis of circuits with ideal switch.
ONTOLOGY-BASED SEMANTIC VERIFICATION FOR UML BEHAVIORAL MODELS
Authors: HE HONGYUE , WANG ZHIXUE , DONG QINGCHAO , ZHANG WEIZHONG , ZHU WEIXING
Published: June 2013

UML is now popularly applied as a requirements modeling language for software system analysis and design, and the dynamic behaviors of system are described in UML behavioral model. As the UML model suffers from lack of well-defined formal semantics, it is difficult to formally analyze and verify the behavioral model. The paper presents a method of UML behavioral model verification based on Description Logic system and its formal inference. The semantics of UML behavioral models is divided into static semantics and dynamic semantics, which are formally specified in OWL DL ontology and DL-Safe rules. To check the consistency of the behavioral models, the algorithms are provided for transforming UML behavioral models into OWL DL ontology, and hence model consistency can be verified through formal reasoning with a DL supporting reasoner Pellet. A case study is provided to demonstrate applicability of the method.
SOFTWARE PERFORMANCE ENGINEERING BY SIMULATED-BASED OBJECT DEPLOYMENT
Authors: BUSHEHRIAN OMID
Published: June 2013

The object deployment of a distributed software has a great impact on its performance. In this paper an analytical model for performance evaluation of different object deployments, is presented. The key advantage of the proposed model over the traditional Queuing Network models is the usefulness in the deployment optimization when the search space is huge and automatic instantiation of Queuing performance models corresponding to an object deployment is costly. Since our model produces an optimal deployment corresponding to each input load separately, the runtime behavior of the software corresponding to each input load should be profiled using simulation first. In this paper a translation scheme for generating the simulate-able Labeled Transition Systems (LTS) from scenarios is also presented. Moreover, two deployment algorithms (a GA-based and an INLP-based) are implemented and the results are compared.
WikiIdRank++: EXTENSIONS AND IMPROVEMENTS OF THE WikiIdRank SYSTEM FOR ENTITY LINKING
Authors: JIMÉNEZ M. D. , FERNÁNDEZ N. , ARIAS FISTEUS J. , SÁNCHEZ L.
Published: June 2013

The amount of information available on the Web has grown considerably in recent years, leading to the need to structure it in order to access it in a quick and accurate way. In order to develop techniques to automate the structuring process, the Knowledge Base Population (KBP) track of the Text Analysis Conference (TAC) was created. This forum aims to encourage research in automated systems capable of capturing knowledge in unstructured information. One of the tasks proposed in the context of the KBP track is named entity linking, and its goal is to link named entities mentioned in a document to instances in a reference knowledge base built from Wikipedia. This paper focuses on the entity linking task in the context of KBP 2010, where two different varieties of this task were considered, depending on whether the use of the text from Wikipedia was allowed or not. Specifically, the paper proposes a set of modifications to a system that participated in KBP 2010, named WikiIdRank, in order to improve its performance. The different modifications were evaluated in the official KBP 2010 corpus, showing that the best combination increases the accuracy of the initial system in a 7.04%. Though the resultant system, named WikiIdRank++, is unsupervised and does not take advantage of Wikipedia text, a comparison with other approaches in KBP indicates that the system would rank as 4th (out of 16) in the global comparison, outperforming other approaches that use human supervision and take advantage of Wikipedia textual contents. Furthermore, the system would rank as 1st in the category of systems that do not use Wikipedia text.
A NUMERICAL APPROACH TO UNCERTAINTY IN ROUGH LOGIC
Authors: SHE YAN-HONG , HE XIAO-LI
Published: June 2013

Rough set theory, initiated by Pawlak, is a mathematical tool in dealing with inexact and incomplete information. Numerical characterizations of rough sets such as accuracy measure, roughness measure, etc, which aim to quantify the imprecision of a rough set caused by its boundary region, have been extensively studied in the existing literatures. However, very few of them are explored from the viewpoint of rough logic, which, however, helps to establish a kind of approximate reasoning mechanism. For this purpose, we introduce a kind of numerical approach to the study of rough logic in this paper. More precisely, we propose the notions of accuracy degree and roughness degree for each formula in rough logic with the intension of measuring the extent to which any formula is accurate and rough, respectively. Then, to measure the degree to which any two formulae are roughly included in each other and roughly similar, respectively, the concepts of rough inclusion degree and rough similarity degree are also proposed and their properties are investigated in detail. Lastly, by employing the proposed notions, we develop two types of approximate reasoning patterns in the framework of rough logic.
ALGAE GROWTH PREDICTION THROUGH IDENTIFICATION OF INFLUENTIAL ENVIRONMENTAL VARIABLES: A MACHINE LEARNING APPROACH
Authors: RAHMAN ASHFAQUR , SHAHRIAR MD SUMON
Published: June 2013

In this paper, we present an approach for predicting algae growth through the selection of influential environmental variables. Chlorophyll a is considered to be an indicator for algal biomass and we predict this as a proxy for algae growth. Environmental variables like water temperature, salinity, etc. have influence upon algae growth. Depending on the geographic location, the influence of these environmental variables will vary. Given a set of relevant environmental variables we perform feature selection using a number of algorithms to identify the variables relevant to the growth. We have developed an influence matrix-based approach to select the relevant features. The selected features are then used for predicting algae growth using different regression algorithms to identify their relative strength. The approach is tested on the algae data of Derwent estuary in Tasmania. The experimental results demonstrate that the accuracy of algae growth prediction with influence matrix-based feature selection is superior to using all the features.
SOME DIFFERENCE SEQUENCE SPACES GENERATED BY DE LA VALLÉE-POUSSIN MEAN
Authors: Srivastava P. D. , Manna Atanu
Published: June 2013

A difference sequence space using φ-function and involving the concept of de la Vallée-Poussin mean is introduced. Inclusion relations, structural and topological properties of this space are investigated. By introducing a modular structure, the equality of the countably and uniformly countably modulared spaces is obtained.
RATIONAL ENERGY BALANCE METHOD TO NONLINEAR OSCILLATORS WITH CUBIC TERM
Authors: Daeichin M. , Ahmadpoor M. A. , Askari H. , Yildirim A.
Published: June 2013

In this paper, a novel approach is proposed for solving the nonlinear problems based on the collocation and energy balance methods (EBMs). Rational approximation is employed as an initial guess and then it is combined with EBM and collocation method for solving nonlinear oscillators with cubic term. Obtained frequency amplitude relationship is compared with exact numerical solution and subsequently, a very excellent accuracy will be revealed. According to the numerical comparisons, this method provides high accuracy with 0.03% relative error for Duffing equation with strong nonlinearity in the second-order of approximation. Furthermore, achieved results are compared with other types of modified EBMs and the second-order of harmonic balance method. It is demonstrated that the new proposed method has the highest accuracy in comparison with different approaches such as modified EBMs and the second-order of harmonic balance method.