bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Authors: Fang Kechi , Zhao Hansheng , Sun Changyue , Lam Carolyn MC , Chang Suhua , Zhang Kunlin , Panda Gurudutta , Godinho Miguel , Martins dos Santos Vítor AP , Wang Jing 
Published: May 2011

Abstract

Background

Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets.

Results
We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, i KF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model i KF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets.

Conclusions
As the first genome-scale metabolic network of B. cenocepacia J2315, i KF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.
Copy number polymorphisms and anticancer pharmacogenomics
Authors: Gamazon Eric R , Huang R Stephanie , Dolan M Eileen , Cox Nancy J 
Published: May 2011

Abstract
Background
Recent studies have investigated the contribution of copy number variants (CNVs) to disease susceptibility in a multitude of complex disorders, including systemic lupus erythematosus, Crohn's disease, and various neurodevelopmental disorders. Relatively few CNV studies, however, have been conducted on pharmacologic phenotypes even though these structural variants are likely to play an important role. We developed a genome-wide method to identify CNVs that contribute to heterogeneity in drug response, focusing on drugs that are widely used in anticancer treatment regimens.

Results
We conducted a comprehensive genome-wide study of CNVs from population-scale array-based and sequencing-based surveys by analyzing their effect on cellular sensitivity to platinating agents and topoisomerase II inhibitors. We identified extensive CNV regions associated with cellular sensitivity to functionally diverse chemotherapeutics, supporting the hypothesis that variation in copy number contributes to variation in drug response. Interestingly, although single nucleotide polymorphisms (SNPs) tag some of the CNVs associated with drug sensitivity, several of the most significant CNV-drug associations are independent of SNPs; consequently, they represent genetic variations that have not been previously interrogated by SNP studies of pharmacologic phenotypes.

Conclusions
Our findings demonstrate that pharmacogenomic studies may greatly benefit from the study of CNVs as expression quantitative trait loci, thus contributing broadly to our understanding of the complex traits genetics of CNVs. We also extend our PACdb resource, a database that makes available to the scientific community relationships between genetic variation, gene expression, and sensitivity to various drugs in cell-based models.
From bouncy legs to poisoned arrows: elastic movements in invertebrates
Authors: Patek S. N. , Dudek D. M. , Rosario M. V. 
Published: May 2011

SummaryElastic mechanisms in the invertebrates are fantastically diverse, yet much of this diversity can be captured by examining just a few fundamental physical principles. Our goals for this commentary are threefold. First, we aim to synthesize and simplify the fundamental principles underlying elastic mechanisms and show how different configurations of basic building blocks can be used for different functions. Second, we compare single rapid movements and rhythmic movements across six invertebrate examples – ranging from poisonous cnidarians to high-jumping froghoppers – and identify remarkable functional properties arising from their underlying elastic systems. Finally, we look to the future of this field and find two prime areas for exciting new discoveries – the evolutionary dynamics of elastic mechanisms and biomimicry of invertebrate elastic materials and mechanics.
Experimentally reduced corticosterone release promotes early breeding in black-legged kittiwakes
Authors: Goutte Aurélie , Clément-Chastel Céline , Moe Børge , Bech Claus , Gabrielsen Geir Wing , Chastel Olivier 
Published: May 2011

SUMMARY
Breeding at the right time is important for successful reproduction. In birds, stressful environmental conditions are known to delay the timing of breeding but the underlying mechanisms are poorly understood. The stress hormone corticosterone appears to be a good candidate for mediating egg-laying date according to early environmental conditions and physiological state. By experimentally reducing the release of corticosterone in black-legged kittiwakes during the pre-laying period, we tested whether egg-laying date was mechanistically linked to corticosterone levels. Male and female kittiwakes were implanted with a low dose of exogenous corticosterone to inhibit endogenous corticosterone production. According to our predictions, the experimental reduction of corticosterone release was paralleled by a significant advancement of egg laying in females (around 4 days earlier). In addition, females with experimentally reduced corticosterone release gained mass during the pre-laying period compared with controls. Ultimately, the advancement of egg laying in females with experimentally reduced corticosterone levels was associated with an enhanced breeding success. This effect was strongly sex specific. In corticosterone-treated male kittiwakes, egg-laying date and reproductive success were not affected, but breeding probability was lower than in controls. This corticosterone treatment did not influence immediate clutch size, or return rate and breeding decision the following year. Our results support the hypothesis that corticosterone secretion during the pre-laying period mediates the timing of breeding in this long-lived seabird, possibly through the dynamics of energy reserves.
The influence of PKA treatment on the Ca2+ activation of force generation by trout cardiac muscle
Authors: Gillis Todd E. , Klaiman Jordan M. 
Published: May 2011

SUMMARY
β-Adrenergic stimulation of the mammalian heart increases heart rate, the strength of contraction as well as the kinetics of force generation and relaxation. These effects are due to the phosphorylation of select membrane and thin filament proteins by cAMP-activated protein kinase (PKA). At the level of the sarcomere, it is typically the phosphorylation of cardiac myosin binding protein C (cMyBP-C) and cardiac troponin I (cTnI) that is responsible for the change in the kinetics of contraction and relaxation. Trout cTnI (ScTnI) lacks two critical PKA targets within the N-terminus of the protein that, when phosphorylated in mammalian cTnI, cause a reduction in myofilament Ca2+ affinity. To determine what role the contractile element plays in the response of the trout heart to β-adrenergic stimulation, we characterized the influence of PKA treatment on the Ca2+ activation of skinned preparations dissected from ventricular trabeculae. In these experiments, isometric force generation and the rate of force development were measured over a range of Ca2+ concentrations. The results demonstrate that PKA treatment does not influence the Ca2+ sensitivity of force generation but it decreases maximum force generation by 25% and the rate of force re-development at maximal activation by 46%. Analysis of the trabeculae preparations for phosphoproteins revealed that PKA treatment phosphorylated myosin light chain 2 but not cTnI or cMyBP-C. These results indicate that the function of the trout cardiac contractile element is altered by PKA phosphorylation but in a manner different from that in mammalian heart.
Energetically optimal stride frequency in running: the effects of incline and decline
Authors: Snyder Kristine L. , Farley Claire T. 
Published: May 2011

SUMMARY
At a given running speed, humans strongly prefer to use a stride frequency near their ‘optimal’ stride frequency that minimizes metabolic cost. Although there is no definitive explanation for why an optimal stride frequency exists, elastic energy usage has been implicated. Because the possibility for elastic energy storage and return may be impaired on slopes, we investigated whether and how the optimal stride frequency changes during uphill and downhill running. Presuming a smaller role of elastic energy, we hypothesized that altering stride frequency would change metabolic cost less during uphill and downhill running than during level running. To test this hypothesis, we collected force and metabolic data as nine male subjects ran at 2.8 m s–1 on the level, 3 deg uphill and 3 deg downhill. Stride frequency was systematically varied above and below preferred stride frequency (PSF ±8% and ±15%). Ground reaction force data were used to calculate potential, kinetic and total mechanical energy, and to calculate the theoretical maximum possible and estimated actual elastic energy storage and return. Contrary to our hypothesis, we found that neither the overall relationship between metabolic cost and stride frequency nor the energetically optimal stride frequency changed substantially with slope. However, estimated actual elastic energy storage as a percentage of total positive power increased with increasing stride frequency on all slopes, indicating that muscle power decreases with increasing stride frequency. Combined with the increased cost of force production and internal work with increasing stride frequency, this leads to an intermediate optimal stride frequency and overall U-shaped curve.
Involvement of redox- and phosphorylation-dependent pathways in osmotic adaptation in sperm cells of euryhaline tilapia
Authors: Morita Masaya , Nakajima Ayako , Takemura Akihiro , Okuno Makoto 
Published: May 2011

SUMMARYSperm cells involved in fertilisation must tolerate hypo-osmotic and hyper-osmotic environments. Euryhaline tilapia (Oreochromis mossambicus) can acclimatise to and reproduce in freshwater and seawater because its sperm are able to adapt to these differing osmotic environments. In this study, we found that the dephosphorylation of sperm proteins in O. mossambicus correlated with the activation of flagellar motility when sperm were exposed to hypotonic or hypertonic conditions, and that differences in phosphorylation may reflect adaptations to a given osmotic environment. Of the sperm proteins that were dephosphorylated, the phosphorylation pattern of an 18 kDa protein, identified as the superoxide anion scavenger Cu/Zn superoxide dismutase (Cu/Zn SOD), was different in freshwater- and seawater-acclimatised tilapia sperm. Cu/Zn SOD was distributed from the sperm head to the flagellum. Additionally, differences were observed between freshwater and seawater tilapia in the nitration of tyrosine residues (which might be mediated by SOD) in sperm flagellar proteins in response to osmotic shock. These results demonstrate that reactive-oxygen-species-dependent mechanisms contribute to both osmotic tolerance and the activation of flagellar motility.
Circumferential spicule growth by pericellular silica deposition in the hexactinellid sponge Monorhaphis chuni
Authors: Wang Xiaohong , Wiens Matthias , Schröder Heinz C. , Jochum Klaus P. , Schloßmacher Ute , Götz Hermann , Duschner Heinz , Müller Werner E. G. 
Published: May 2011

SUMMARY
The giant basal spicule of the hexactinellid sponge Monorhaphis chuni represents the longest natural siliceous structure on Earth. This spicule is composed of concentrically arranged lamellae that are approximately 10 μm thick. In the present study, we investigated the formation of outer lamellae on a cellular level using microscopic and spectroscopic techniques. It is shown that the formation of an outermost lamella begins with the association of cell clusters with the surface of the thickening and/or growing spicule. The cells release silica for controlled formation of a lamella. The pericellular (silica) material fuses to a delimited and textured layer of silica with depressions approximately 20–30 μm in diameter. The newly formed layer initially displays 40 μm wide, well-structured banded ribbons and only attains its plain surface in a final step. The chemical composition in the depressions was studied using energy dispersive X-ray spectroscopy and by staining with Texas Red. The data suggest that those depressions are the nests for the silica-forming cells and that silica formation starts with a direct association of silica-forming cells with the outer surface of the spicule, where they remain and initiate the development of the next lamellae.
Extraction of Cu(II) Based on Tube Radial Distribution of Ternary Mixed Carrier Solvent in Microchannels
Authors: Jinno Naoya , Hashimoto Masahiko , Tsukagoshi Kazuhiko 
Published: May 2011

Abstract
The extraction of Cu(II) as a model was examined based on tube radial distribution of a ternary mixed carrier solution of water–acetonitrile–ethyl acetate (2:3:1 volume ratio) in a microchannel in a microchip. A microchip incorporating microchannels in which one wide channel was separated into three narrow channels was designed and manufactured. When the ternary carrier solution was fed into the wide channel under laminar flow conditions, the carrier solvent molecules were radially distributed in the channel, generating inner (organic solvent-rich major) and outer (water-rich minor) phases. The Cu(II) dissolved in the carrier solution was distributed between the inner and outer phases due to its hydrophilic nature and then collected through the three narrow channels. The concentrations of Cu(II) in the two side narrow channels were greater than that in the center narrow channel through extraction.
Synthesis and Characterization of a Novel Ruthenium Complex Bearing a Curcumin Derivative Ligand and Its Application to Dye-sensitized Solar Cells
Authors: Ozawa Hironobu , Kawaguchi Hiroki , Okuyama Yu , Arakawa Hironori 
Published: May 2011

Abstract
A novel ruthenium complex bearing a bisdemethoxycurcumin, which is a natural dye exhibiting a strong absorption around 410 nm, as a ligand has been synthesized and characterized for application to dye-sensitized solar cells (DSCs). The DSC with this sensitizer showed about 55% incident photon-to-current conversion efficiency at the wavelength region between 450 and 600 nm, and 5.76% conversion efficiency under AM 1.5 (100 mW cm−2) irradiation.
COFFERDAMS.
Authors: PACKSHAW S 
Published: May 2011

The functions of cofferdams are defined, and their types are divided into two main classifications: the first constructed of soil, concrete or timber, and the second depending primarily on steel sheet piling. These are further sub-divided and listed in two charts. The choice available to the designer is discussed in relation to the permanent structure to be built within the dam, the site conditions, the depth of the cofferdam and the nature of the ground. For design purposes cofferdamas re divided into two categories, namely singleskin and doubleskin, the latter including cellular cofferdams. The basic principles are discussed and attention is drawn to certain aspects of the design of cofferdams in both categories. Graphs for use in the preparation of preliminary designs and estimates for cofferdams of conventional construction are given. Finally, the mechanisms of failure of cofferdams are reviewed. Reference is made to the fact that they are generally derived from the inability of the ground inside the cofferdam to withstand the external forceasn d not fromth e structural failure of the materials used in the construction.
Effect of three different motivational techniques on oral hygiene and gingival health of patients undergoing multibracketed orthodontics
Authors: Acharya Shivesh , Goyal Ashima , Utreja Ashok Kumar , Mohanty Utkal 
Published: May 2011

Abstract

Objective:
To compare the effectiveness of three different motivational techniques for maintaining good oral hygiene during fixed appliance orthodontic treatment.

Materials and Methods:
A total of 62 adolescents in the age range of 12–18 years, requiring fixed orthodontic treatment were evaluated for the efficacy of three different motivational techniques, ie, conventional plaque control measures (group I), chair side motivational tests with conventional plaque control measures (group II), and phase contrast microscopy with conventional plaque control measures (group III), in improving oral hygiene and gingival health over a period of 6 months.

Results:
A gradual decline in mean plaque scores in group III was found, ie, from 1.13 ± 0.42 at baseline to 0.64 ± 0.39 at 6 months (P &lt; .05). An intragroup analysis of mean gingivitis scores in group III showed statistically significant decline in the mean gingival scores from 1.49 ± 0.45 to 1.08 ± 0.61 over a period of 6 months(P &lt; .05).

Conclusions:
Phase contrast microscopy along with the conventional method of plaque disclosure and demonstration of the horizontal scrubbing method of brushing have a long-lasting effect on the patient. This reduces the need of frequent reinforcement sessions of plaque control programs when compared to chair side motivational tests and conventional plaque control measures.
Long-Term Outcome of Individuals Treated With Oral Insulin
Authors: Vehik Kendra , Cuthbertson David , Ruhlig Holly , Schatz Desmond A. , Peakman Mark , Krischer Jeffrey P. ,   for the DPT-1 and TrialNet Study Groups
Published: May 2011

OBJECTIVETo evaluate the long-term intervention effects of oral insulin on the development of type 1 diabetes and to assess the rate of progression to type 1 diabetes before and after oral insulin treatment was stopped in the Diabetes Prevention Trial–Type 1 (DPT-1).RESEARCH DESIGN AND METHODSThe follow-up included subjects who participated in the early intervention of oral insulin (1994–2003) to prevent or delay type 1 diabetes. A telephone survey was conducted in 2009 to determine whether diabetes had been diagnosed and, if not, an oral glucose tolerance test (OGTT), hemoglobin A1c (HbA1c), and autoantibody levels were obtained on all subjects who agreed to participate.RESULTSOf 372 subjects randomized, 97 developed type 1 diabetes before follow-up; 75% of the remaining 275 subjects were contacted. In the interim, 77 subjects had been diagnosed with type 1 diabetes and 54 of the remainder have had an OGTT; 10 of these were diagnosed with type 1 diabetes, subsequently. Among individuals meeting the original criteria for insulin autoantibodies (IAAs) (≥80 nU/mL), the overall benefit of oral insulin remained significant (P = 0.05). However, the hazard rate in this group increased (from 6.4% [95% CI 4.5–9.1] to 10.0% [7.1–14.1]) after cessation of therapy, which approximated the rate of individuals treated with placebo (10.2% [7.1–14.6]).CONCLUSIONSOverall, the oral insulin treatment effect in individuals with confirmed IAA ≥80 nU/mL appeared to be maintained with additional follow-up; however, once therapy stopped, the rate of developing diabetes in the oral insulin group increased to a rate similar to that in the placebo group.
Magnetomotive cooling and excitation of carbon nanotube oscillations under voltage bias
Authors: Nordenfelt Anders 
Published: May 2011

Abstract
We explore a semi-classical scheme for cooling and excitation of mechanical oscillations of a suspended carbon nanotube which is incorporated as a deflection-sensitive resistor in an LRC-circuit. The active feedback consists of a magnetically induced Lorentz force. We show that, for feasible experimental parameters, we can obtain self-sustained oscillations or cooling by several orders of magnitude.
Diameter of the ductus arteriosus as a predictor of patent ductus arteriosus (PDA)
Authors: Nowak Dariusz , Kozłowska Hanna , Żurada Anna , Gielecki Jerzy 
Published: May 2011

Abstract
Patent ductus arteriosus (PDA) is the most prevalent cardiovascular defect and is more often seen in females; premature babies are at increased risk. For both sexes, a relationship exists between the risk of this defect occurring and the higher dimensions of the ductus arteriosus. In this study, we examined the relationship between the dimensions of the ductus arteriosus (diameter, length, capacity) and sex. We analyzed a total of 223 fetuses, 108 males and 115 females, ranging in age from four to eight months of intrauterinal life. All fetuses of normal karyotype were obtained from spontaneous abortions. None of the analyzed specimens demonstrated any visible malformations. The increase in the length and diameters of the ductus is linearly related to gestational age. The volumetric growth of this vessel was dependent on fetal age, according to the exponential function. The large number of analyzed specimens allows reliable determination of the ductus arteriosus dimensions in consecutive months of fetal life. The data obtained could be of prognostic value during echocardiographic follow-up in the fetus. We found that the dimensions analyzed did not differ with regard to sex. It is a contradiction that, more frequently PDA in females is caused with the gender differences in the dimensions of ductus arteriosus.
Environmentally benign one-pot synthesis and antimicrobial activity of 1-methyl-2,6-diarylpiperidin-4-ones
Authors: Nithya Pattusamy , Nawaz Khan Fazlur-Rahman , Roopan Selvaraj , Shankar Uma , Jin Jong 
Published: May 2011

AbstractAn efficient and environmentally benign one-pot method for the synthesis of 1-methyl-2,6-diarylpiperidin-4-ones using montmorillonite K-10 as a catalyst has been developed. Antimicrobial activity of the compounds has been tested against selected representatives of Gram-positive and Gram-negative bacteria and fungi.
Covariate Measurement Error Adjustment for Multilevel Models With Application to Educational Data
Authors: Battauz Michela , Bellio Ruggero , Gori Enrico 
Published: May 2011

This article proposes a multilevel model for the assessment of school effectiveness where the intake achievement is a predictor and the response variable is the achievement in the subsequent periods. The achievement is a latent variable that can be estimated on the basis of an item response theory model and hence subject to measurement error. Ignoring covariate measurement error leads to biased parameter estimates. To address this problem, a likelihood-based measurement error adjustment for multilevel models is proposed. In particular, the method deals with a covariate measured with error that has a random coefficient. An application to educational data from the Italian region of Lombardy illustrates the method. Manuscript received January 21, 2009 Revision received November 24, 2009 Accepted January 17, 2010