bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of 1‐methylcyclopropene in lignification and expansin gene expression in peeled water bamboo shoot (Zizania caduciflora L.)
Authors: Song Lili , Gao Haiyan , Chen Wenxuan , Chen Hangjun , Mao Jinlin , Zhou Yongjun , Duan Xuewu , Joyce Daryl C
Published: July 2011

BACKGROUND: Water bamboo shoot (WBS) (Zizania caduciflora L.) is a fleshy aquatic vegetable susceptible to lignification. In this study, effects of 1‐methylcyclopropene (1‐MCP) anti‐ethylene treatment on lignification of harvested peeled WBS were investigated.

RESULTS: Peeled shoots were treated with 0.5 µL L−1 1‐MCP for 20 h at 20 °C and then stored at 20 °C for up to 9 days. Sensory quality, lignin content and activities of the lignification‐associated enzymes peroxidase (POD) and phenylalanine ammonia lyase (PAL) were evaluated. Expression of expansin (ZcExp) was also assessed. 1‐MCP application maintained better sensory quality and inhibited the increase in lignin content. Lessened lignification was associated with reduced activities of POD and PAL. Moreover, 1‐MCP‐treated shoots showed lower expression of the ZcExp gene.

CONCLUSION: 1‐MCP pretreatment suppressed the synthesis of lignin and thereby delayed lignification in peeled WBS. Copyright © 2011 Society of Chemical Industry
Comparison of adaptive neuro‐fuzzy inference system and artificial neural networks for estimation of oxidation parameters of sunflower oil added with some natural byproduct extracts
Authors: Karaman Safa , Ozturk Ismet , Yalcin Hasan , Kayacier Ahmed , Sagdic Osman
Published: July 2011

BACKROUND: Apple pomace, orange peel and potato peel, which have important antioxidative compounds in their structures, are byproducts obtained from fruit or vegetable processing. Use of vegetable extracts is popular and a common technique in the preservation of vegetable oils. Utilization of apple pomace, orange peel and potato peel extracts as natural antioxidant agents in refined sunflower oil during storage in order to reduce or retard oxidation was investigated. All byproduct extracts were added at 3000 ppm to sunflower oil and different nonlinear models were constructed for the estimation of oxidation parameters.

RESULTS: Peroxide values of sunflower oil samples containing different natural extracts were found to be lower compared to control sample. Adaptive neuro‐fuzzy inference system (ANFIS) and artificial neural networks (ANN) were used for the construction of models that could predict the oxidation parameters and were compared to multiple linear regression (MLR) for the determination of the best model with high accuracy. It was shown that the ANFIS model with high coefficient of determination (R2 = 0.999) performed better compared to ANN (R2 = 0.899) and MLR (R2 = 0.636) for the prediction of oxidation parameters

CONCLUSION: Incorporation of different natural byproduct extracts into sunflower oil provided an important retardation in oxidation during storage. Effective predictive models were constructed for the estimation of oxidation parameters using ANFIS and ANN modeling techniques. These models can be used to predict oxidative parameter values. Copyright © 2011 Society of Chemical Industry
Assessment of polyelectrolyte coating stability under dynamic buffer conditions in CE
Authors: Swords Kyleen E. , Bartline Peter B. , Roguski Katherine M. , Bashaw Sarah A. , Frederick Kimberley A.
Published: July 2011

Dynamic buffer conditions are present in many electrophoretically driven separations. Polyelectrolyte multilayer coatings have been employed in CE because of their chemical and physical stability as well as their ease of application. The goal of this study is to measure the effect of dynamic changes in buffer pH on flow using a real‐time method for measuring EOF. Polyelectrolyte multilayers (PEMs) were composed of pairs of strong or completely ionized polyelectrolytes including poly(diallyldimethylammonium) chloride and poly(styrene sulfonate) and weak or ionizable polyelectrolytes including poly(allylamine) and poly(methacrylic acid). Polyelectrolyte multilayers of varying thicknesses (3, 4, 7, 8, 15, or 16 layers) were also studied. While the magnitude of the EOF was monitored every 2 s, the buffer pH was exchanged from a relatively basic pH (7.1) to increasingly acidic pHs (6.6, 6.1, 5.5, and 5.1). Strong polyelectrolytes responded minimally to changes in buffer pH (<1%), whereas substantial (>10%) and sometimes irreversible changes were measured with weak polyelectrolytes. Thicker coatings resulted in a similar magnitude of response but were more likely to degrade in response to buffer pH changes. The most stable coatings were formed from thinner layers of strong polyelectrolytes.
Spatial and temporal factors influencing sightability of elk
Authors: Wal Eric Vander , McLoughlin Philip D. , Brook Ryan K.
Published: July 2011

Few tracking studies consider seasonal changes in ability to re‐sight wildlife, despite potential for biases in sightability to mislead our interpretation of models of movement and abundance. We developed seasonal sightability models based on visual observations of radio‐collared elk (Cervus elaphus) in Manitoba, Canada, through 6 seasons. We located 377 elk 8,862 times using aerial telemetry from 2002 to 2009. We tested the hypothesis that sites where we were able to visually observe radio‐collared elk during aerial telemetry differed from sites where collared elk were known to be present but could not be sighted. Relationships varied with season and elk sightability was influenced by forest type, habitat openness, distance to edge, and time of day. Our results confirm that observers have the highest probability of detecting elk in early and late winter. However, factors such as day length, which increases by 64% during this period, suggest that fewer impediments to detection exist in late winter. Our findings reinforce the need to account for seasonal as well as spatial changes in habitat‐specific sightability models. © 2011 The Wildlife Society.
Hepatic Steatosis at 1 Year is an Additional Predictor of Subsequent Fibrosis Severity in Liver Transplant Recipients with Recurrent Hepatitis C Virus†
Authors: Brandman Danielle , Pingitore Andrea , Lai Jennifer C. , Roberts John P. , Ferrell Linda , Bass Nathan M. , Terrault Norah A.
Published: July 2011

Recurrent hepatitis C virus (HCV) is the most common cause of graft loss for HCV-infected recipients of liver transplantation (LT). Diabetes mellitus (DM) has been associated with increased rates of fibrosis progression, but whether steatosis affects post-LT outcomes independently of DM is unclear. Using a retrospective cohort of HCV-infected LT recipients, we determined the prevalence of hepatic steatosis and evaluated the relationship between steatosis on index biopsy 1 year after LT (±6 months) and the severity of the subsequent fibrosis. One hundred fifty-two LT recipients with HCV were followed up for a median of 2.09 years (range = 0.13-6.17 years) after index biopsy; the median number of biopsy procedures per patient after index biopsy was 2 (range = 1-6). Steatosis (≥5%) was present in 45 individuals (29.6%) according to index biopsy samples taken 1 year after LT; the steatosis was mild (grade 1) in 80% of the patients. In the multivariate analysis, the presence of steatosis 1 year after LT was positively associated with HCV genotype 3 [odds ratio (OR) = 3.60, P = 0.02], older donor age (OR = 1.03, P = 0.04), and pre-LT hypertension (OR = 3.29, P = 0.009). Two years after index biopsy, the cumulative rate of significant fibrosis (F2-F4 on the Ludwig-Batts scale) was 49% in the patients with steatosis at 1 year and 24% in the patients without steatosis (P = 0.003). In the multivariate analysis, steatosis at 1 year was an independent predictor of subsequent F2 to F4 fibrosis (HR = 2.63, 95% CI = 1.49-4.63). Steatosis was a stronger predictor of fibrosis in the setting of sirolimus use (hazard ratio = 9.38, 95% confidence interval = 1.37-64.16, P = 0.02). In conclusion, steatosis is frequent in the early post-LT period, and steatosis within the first year after LT is a marker of a higher risk of fibrosis progression in HCV-infected patients. Liver Transpl, 2011. © 2011 AASLD.
Endogenous TWIST expression and differentiation are opposite during human muscle development
Authors: Koutsoulidou Andrie , Mastroyiannopoulos Nikolaos P. , Furling Denis , Uney James B. , Phylactou Leonidas A.
Published: July 2011

TWIST is a transcription factor expressed during early embryonic development. In this study we investigate the expression of TWIST during human muscle development. Human TWIST was found to be endogenously expressed in human fetal myoblasts, and its expression decreased during late stages of development. Myoblasts showed an increasing capacity to differentiate in vitro during development. This inversely proportional relation between TWIST and differentiation capacity of myoblasts suggests that TWIST is involved in the regulation of muscle development. Muscle Nerve, 2011
A practical and efficient numerical scheme for the analysis of steady state unconfined seepage flows
Authors: Bazyar Mohammad Hossein , Graili Adel
Published: July 2011

The scaled boundary finite‐element method (SBFEM), a novel semi‐analytical technique, is applied to the analysis of the confined and unconfined seepage flow. This method combines the advantages of the finite‐element method and the boundary element method. In this method, only the boundary of the domain is discretized; no fundamental solution is required, and singularity problems can be modeled rigorously. Anisotropic and nonhomogeneous materials satisfying similarity are modeled without additional efforts. In this paper, SBFE equations and solution procedures for the analysis of seepage flow are outlined. The accuracy of the proposed method in modeling singularity problems is demonstrated by analyzing seepage flow under a concrete dam with a cutoff at heel. As only the boundary is discretized, the variable mesh technique is advisable for modeling unconfined seepage analyses. The accuracy, effectiveness, and efficiency of the method are demonstrated by modeling several unconfined seepage flow problems. Copyright © 2011 John Wiley & Sons, Ltd.
When satire is serious: how political cartoons impact a country's brand
Authors: Bigi Alessandro , Plangger Kirk , Bonera Michelle , Campbell Colin L.
Published: July 2011

This article examines the case of Italy's Mr. Berlusconi's indiscretions and the effect his scandals have played in the decline of the Italian national brand. National brands are the perceived added value that international consumers place on that country and its products and services. An analysis of recent political cartoons will provide insight into international attitudes regarding Mr. Berlusconi's political and social actions. From this investigation, the authors conclude that a country's political leader's negative image and reputation can have a large negative impact on national brand equity abroad. Copyright © 2011 John Wiley & Sons, Ltd.
Modulation of absorption and fluorescence of photochromic diarylethene by intramolecular hydrogen bond
Authors: Liu Huan‐Huan , Chen Yi
Published: July 2011

Photochromic diarylethenes bearing an intramolecular hydrogen bond in bridge moiety have been prepared. It is found that intramolecular hydrogen bonding has a great effect on both absorption and fluorescence of diarylethenes. The color change of diarylethenes in a wide range (purple, blue and green) can be achieved by simple modification of the electronic properties of substituents in bridge moiety, and fluorescent diarylethenes are also obtained when diarylethenes bear an intramolecular hydrogen bond in bridge moiety. Copyright © 2011 John Wiley & Sons, Ltd.
Disproportionating versus nondisproportionating solvent effect in the SET‐LRP of methyl acrylate during catalysis with nonactivated and activated cu(0) wire
Authors: Nguyen Nga H. , Percec Virgil
Published: July 2011

The disproportionating solvent effect on the kinetics of single electron transfer living radical polymerization (SET‐LRP) during catalysis with nonactivated Cu(0) wire coated with Cu2O and activated Cu(0) wire free of Cu2O was studied. In solvents such as dimethyl sulfoxide, MeOH and ethylene carbonate that in conjunction with Me6‐TREN promote extensitve disproportionation of Cu(I)X, faster polymerizations were achieved upon switching from nonactivated Cu(0) wire to activated Cu(0) wire. The results showed that the substantial rate enhancement was accompanied with excellent control of molecular weight evolution and distribution, and high fidelity of chain‐end functionality. This can be attributed to a more effective equilibrium between activation and deactivation in the presence of Cu(0) free of Cu2O. In nondisproportionating solvents, the kinetics of SET‐LRP of methyl acrylate catalyzed by activated Cu(0) wire resembled that of the polymerizations catalyzed by nonactivated wire. This is the result of a competing effect between rapid activation and insufficient disproportionation. The absence of disproportionation effectively leads to the lack of first order kinetics, broad molecular weight distribution, significant loss of bromide chain‐end functionality, and therefore, the absence of a living polymerization. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Yukawa couplings in F‐theory SU(5)
Authors: Leontaris G.K.
Published: July 2011

The fermion mass textures are discussed in the context of F‐theory SU(5) GUT. The tree‐level up, down and charged lepton Yukawa couplings are computed in terms of the integrals of overlapping wavefunctions at the intersection points of three matter curves. All remaining entries in the fermion mass matrices can also be reliably estimated from higher order non‐renormalizable Yukawa couplings mediated by heavy string modes and/or Kaluza‐Klein states.
A Mellin space program for W± and Z0 production at NNLO
Authors: Kovačíková P.
Published: July 2011

We present a program for the evaluation of full unpolarized cross sections for the W± and Z0 production in the narrow width approximation at NNLO in perturbative QCD using Mellin space techniques.
Investigating the potential of selected natural compounds to increase the potency of pyrethrum against houseflies Muscadomestica (Diptera: Muscidae)
Authors: Joffe Tanya , Gunning Robin V , Allen Geoff R , Kristensen Michael , Alptekin Selcan , Field Linda M , Moores Graham D
Published: July 2011

BACKGROUND: A study was undertaken to determine the efficacy of seven natural compounds compared with piperonyl butoxide (PBO) in synergising pyrethrum, with the intention of formulating an effective natural synergist with pyrethrum for use in the organic crop market.

RESULTS: Discriminating dose bioassays showed PBO to be significantly more effective at synergising pyrethrum in houseflies than the seven natural compounds tested, causing 100% mortality in insecticide‐susceptible WHO and resistant 381zb strains of housefly. The most effective natural synergists against WHO houseflies were dillapiole oil, grapefruit oil and parsley seed oil, with 59, 50 and 41% mortality respectively, compared with 18% mortality with unsynergised pyrethrum. Against 381zb houseflies, the most effective natural synergists were parsley seed oil and dillapiole oil. Esterase inhibition by the natural compounds and PBO in vitro showed no correlation with pyrethrum synergism in vivo, whereas the inhibition of oxidases in vitro more closely correlated with pyrethrum synergism in vivo.

CONCLUSION: Dillapiole oil and parsley seed oil showed the greatest potential as pyrethrum synergists. PBO remained the most effective synergist, possibly owing to its surfactant properties, enhancing penetration of pyrethrins. The results suggest the involvement of oxidases in pyrethroid resistance in houseflies, with the efficacy of synergists showing a high correlation with inhibition of oxidases. Copyright © 2011 Society of Chemical Industry
Catalyst free self‐organized grown high‐quality GaN nanorods
Authors: Aschenbrenner T. , Kunert G. , Freund W. , Kruse C. , Figge S. , Schowalter M. , Vogt C. , Kalden J. , Sebald K. , Rosenauer A. , Gutowski J. , Hommel D.
Published: July 2011

Highly ordered GaN nanorods were grown self‐organized and without catalyst on r‐plane sapphire by molecular beam epitaxy while the AlN nucleation sites for the nanorods were provided by a nitridation process using a metal‐organic vapor‐phase epitaxy system. The growth window for the nanorod formation was analysed in detail and turned out to be very sensitive with respect to the growth temperature. The nanorods are symmetrically tilted with an inclination angle of 62° between the substrate and the nanorods. The mirror axis is the c‐direction of the compact GaN layer surrounding the roots of the nanocolumns. Methods for the control of the nanorod density and the suppression of one nanorod growth direction are presented. The results indicate a diffusion based growth mechanism. Transmission electron microscopy studies and high resolution X‐ray diffraction (HRXRD) polar plots reveal the epitaxial relationship between substrate, compact GaN layer and nanorods. The nanorods grow in c‐direction and the side facets are m‐planes. Transmission electron microscopic and optical analysis of the nanorods reveal the good structural and optical properties, respectively. A full width at half maximum (FWHM) of 1.2 meV of the donor‐bound exciton emission was measured for both the ensemble and single free‐standing nanorods. Successful n‐ and Mg‐doping of nanorods was verified by a strong increase of the micro‐photoluminescence intensity of the respective donor‐bound and acceptor‐bound exciton emission peak in comparison to an undoped sample.

magnified image

The background shows a secondary electron microscope image (angle of 10° between sample surface and electron beam) of the nanorods. Superimposed to the SEM image, a typical micro‐photoluminescence spectrum of the excitonic emission of an ensemble at 25 K is presented. The donor‐bound, acceptor‐bound and free exciton lines are labelled with D0X, A0X and FX, respectively.
Delocalization errors in a hubbard‐like model: Consequences for density‐functional tight‐binding calculations of molecular systems
Authors: Lundberg Marcus , Nishimoto Yoshio , Irle Stephan
Published: July 2011

It has previously been shown that self‐consistent‐charge density‐functional tight‐binding (SCC‐DFTB) suffers from a self‐interaction error that leads to artificial stabilization of delocalized states. The effects of the error are similar to those appearing for many density functionals. In SCC‐DFTB, the delocalization error is inherently related to the use of a Hubbard‐like term to describe on‐site charge interactions. The mathematical simplicity of this Hubbard‐like term makes it easy to estimate if a complex system is subject to artificial stabilization of delocalized states and to quantitatively predict the delocalization error in the system energy at large fragment separation. The error is directly proportional to the on‐site charge interaction term but decreases as the fragments become more asymmetric. The difference in orbital energies required to eliminate the delocalization error becomes equal to the Hubbard‐like parameter of the fragment with the highest electron affinity. However, in most cases, the localized state will be favored by spin polarization, fragment repulsion, solvent effects, and large reorganization energies, in analogy to density functional theory, from which SCC‐DFTB is derived. The presented analysis gives an early indication whether the standard approach is suitable, or if a different method is required to correct the delocalization error. In addition to cationic dimers, we discuss the effects of the delocalization error for asymmetric systems, bond dissociation of neutral molecules, and the description of mixed valence transition metal systems, exemplified by the enzyme cytochrome oxidase. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Quantification of the transporter substrate fexofenadine in cell lysates by liquid chromatography/tandem mass spectrometry
Authors: Flynn Colleen A. , Alnouti Yazen , Reed Gregory A.
Published: July 2011

Drug–drug interactions at transporters present a significant and under‐investigated clinical problem. Investigations of specific transporter functions and screening for potential drug‐drug interactions, both in vitro and especially in vivo, will require validated experimental probes. Fexofenadine, an approved, well‐tolerated drug, is a promising probe for studies of membrane transporter function. Although fexofenadine pharmacokinetics are known to be controlled by transporters, the contributions of individual transporters have not been defined. We have developed a rapid, specific, and sensitive analytical method for quantitation of fexofenadine to support this work. This liquid chromatography/tandem mass spectrometry (LC/MS/MS) method quantifies fexofenadine in cell lysates from in vitro studies using cetirizine as the internal standard. Cell lysates were prepared for analysis by acetonitrile precipitation. Analytes were then separated by gradient reversed‐phase chromatography and analyzed by tandem mass spectrometry using the m/z 502.17/466.2 transition for fexofenadine and m/z 389.02/201.1 for cetirizine. The method exhibited a linear dynamic range of 1–500 ng/mL for fexofenadine in cell lysates. The lower limit of quantification was 1 ng/mL with a relative standard deviation of less than 5%. Intra‐ and inter‐day precision and accuracy were within the limits presented in the FDA guidelines for bioanalysis. We also will validate this method to support not only the quantification of fexofenadine, but also other probe drugs for drug–drug interaction studies. This method for quantification will facilitate the use of fexofenadine as a probe drug for characterization of transporter activity. Copyright © 2011 John Wiley & Sons, Ltd.
EFFECTS OF ARTIFICIAL FLOODING ON WATER QUALITY OF A FLOODPLAIN BACKWATER
Authors: Lizotte R. E. , Shields F. D. , Knight S. S. , Cooper C. M. , Testa S. , Bryant C. T.
Published: July 2011

Seasonal flooding of riverine backwaters is important in maintaining diverse aquatic habitats, but anthropogenic impacts have reduced the frequency and duration of such flooding. This study, conducted in a 2.5‐km‐long shallow floodplain severed meander backwater adjacent to the Coldwater River in Tunica County, Mississippi, USA, compared water quality during a late summer 30‐day artificial flooding period with 28‐day pre‐flood and 26‐day post‐flood periods. Flooding was simulated by pumping 0.22 to 0.35 m3 s−1 from the river into the upstream portion of the backwater. In situ parameters (temperature, pH, dissolved oxygen, conductivity and fluorescent chlorophyll) were measured every 30 min at one site within the backwater. Solids (dissolved and suspended) and nutrients (phosphorus and nitrogen) were measured at three sites in the backwater and in the river every 3 to 5 days. Decreases in the amplitude of temperature, dissolved oxygen and pH diel cycles within the backwater were observed during flooding. Changes in patterns of solids and nutrients were also associated with flooding. Complex patterns in phosphorus and nitrogen emerged as a result of utilization by autotrophs (measured as chlorophyll) and seasonal changes. Artificial flooding in a shallow floodplain water body stabilized and improved water quality for aquatic biota and is a viable method for habitat rehabilitation in these systems. Copyright © 2011 John Wiley & Sons, Ltd.
ELECTRICAL RESISTANCE SENSOR ARRAYS AS A MEANS TO QUANTIFY LONGITUDINAL CONNECTIVITY OF RIVERS
Authors: Jaeger K. L. , Olden J. D.
Published: July 2011

Electrical resistance sensors are used as a novel approach to quantify streamflow continuity (continuous through time) and longitudinal connectivity (continuous through space) across watersheds in south‐eastern Arizona, USA. We demonstrate this approach by reporting on a spatial array of 21 sensors installed in streams supporting naturally perennial, intermittent and ephemeral flow on the US Army Garrison, Fort Huachuca. Continuity and connectivity were quantified based on a strict interpretation of continuous flow at an individual sensor (strict continuity) or simultaneous streamflow at multiple sensors (strict connectivity). In addition, we evaluated continuity and connectivity to include periods (<48 h) when in‐channel refuges may exist between streamflow events (refuge‐maintained continuity and connectivity). Continuous streamflow in intermittent reaches accounted for 34% of the 121‐day monitoring period (15 April–13 August 2010) and 28% of the summer monsoon period (1 July–13 August 2010). Streamflow in ephemeral reaches accounted for 1.5% and 2.3% of the entire monitoring and monsoon period, respectively. Canyon‐wide longitudinal connectivity was rare (<1%); however, substantial longitudinal connection occurred along extensive portions of individual canyons. The refuge‐maintained criteria increased continuity 2–8%, with less influence on connectivity (e.g. <3% increase in only some portions of canyons). Despite this result, the refuge‐maintained concept remains important because of its broad applicability to refuge persistence across aquatic species and hydro‐climatic regimes. The approach presented in this study supports the growing scientific research on the influence of longitudinal hydrologic connectivity on population dynamics and ecological processes in dendritic river networks. Copyright © 2011 John Wiley & Sons, Ltd.
AN EVALUATION OF THE RELATIVE QUALITY OF DIKE POOLS FOR BENTHIC MACROINVERTEBRATES IN THE LOWER MISSOURI RIVER, USA
Authors: Poulton B. C. , Allert A. L.
Published: July 2011

A habitat‐based aquatic macroinvertebrate study was initiated in the Lower Missouri River to evaluate relative quality and biological condition of dike pool habitats. Water‐quality and sediment‐quality parameters and macroinvertebrate assemblage structure were measured from depositional substrates at 18 sites. Sediment porewater was analysed for ammonia, sulphide, pH and oxidation–reduction potential. Whole sediments were analysed for particle‐size distribution, organic carbon and contaminants. Field water‐quality parameters were measured at subsurface and at the sediment–water interface. Pool area adjacent and downstream from each dike was estimated from aerial photography. Macroinvertebrate biotic condition scores were determined by integrating the following indicator response metrics: % of Ephemeroptera (mayflies), % of Oligochaeta worms, Shannon Diversity Index and total taxa richness. Regression models were developed for predicting macroinvertebrate scores based on individual water‐quality and sediment‐quality variables and a water/sediment‐quality score that integrated all variables. Macroinvertebrate scores generated significant determination coefficients with dike pool area (R2 = 0.56), oxidation–reduction potential (R2 = 0.81) and water/sediment‐quality score (R2 = 0.71). Dissolved oxygen saturation, oxidation–reduction potential and total ammonia in sediment porewater were most important in explaining variation in macroinvertebrate scores. The best two‐variable regression models included dike pool size + the water/sediment‐quality score (R2 = 0.84) and dike pool size + oxidation–reduction potential (R2 = 0.93). Results indicate that dike pool size and chemistry of sediments and overlying water can be used to evaluate dike pool quality and identify environmental conditions necessary for optimizing diversity and productivity of important aquatic macroinvertebrates. A combination of these variables could be utilized for measuring the success of habitat enhancement activities currently being implemented in this system. Published in 2011 by John Wiley & Sons, Ltd.
Three‐dimensional electron microscopy simulation with the CASINO Monte Carlo software
Authors: Demers Hendrix , Poirier‐Demers Nicolas , Couture Alexandre Réal , Joly Dany , Guilmain Marc , de Jonge Niels , Drouin Dominique
Published: July 2011

Monte Carlo softwares are widely used to understand the capabilities of electron microscopes. To study more realistic applications with complex samples, 3D Monte Carlo softwares are needed. In this article, the development of the 3D version of CASINO is presented. The software feature a graphical user interface, an efficient (in relation to simulation time and memory use) 3D simulation model, accurate physic models for electron microscopy applications, and it is available freely to the scientific community at this website:www.gel.usherbrooke.ca/casino/index.html. It can be used to model backscattered, secondary, and transmitted electron signals as well as absorbed energy. The software features like scan points and shot noise allow the simulation and study of realistic experimental conditions. This software has an improved energy range for scanning electron microscopy and scanning transmission electron microscopy applications. SCANNING 33:135–146, 2011. © 2011 Wiley Periodicals, Inc.
Synthesis and properties of carboxymethyl Pueraria thomsonii Benth. starch
Authors: Jiang Qianqian , Gao Wenyuan , Li Xia , Liu Zhen , Huang Luqi , Xiao Peigen
Published: July 2011

As a source of starch, Pueraria thomsonii Benth. was selected to synthesize carboxymethyl starch (CMS) with monochloroacetic acid (MCA) in the presence of sodium hydroxide for the first time. The influence of the molar ratio of NaOH/AGU and MCA/AGU, reaction time, temperature, and water content of solvent on the degree of substitution and reaction efficiency were studied. IR spectrometry showed bands at 1609, 1420, and 1369 cm−1 due to –COO− symmetric and asymmetric stretching vibration when starch was successfully substituted. The SEM results displayed that the granules were agglomerate, and curly wrinkles appeared upon carboxymethylation. XRD revealed that the crystallinity reduced from 41.45 to 5.91%. Furthermore, the 13C NMR spectra of the CMS showed a broad band at d = 178.85 ppm, which was assigned to the –CO carbon (C‐8) of the carboxymethyl group.
The solution of system of integral differential equations and its application in the theory of elasticity
Authors: Shavlakadze N.
Published: July 2011

A contact problem of the theory of elasticity of infinite compound and infinite orthotropic plates with an elastic semi‐infinite or finite inclusion of variable rigidity is considered. The problem is reduced to the system of integral differential equations with variable coefficient of singular operator. If such coefficient varies with power law we can manage to investigate the obtained equations, using the methods of analytical functions to get exact solutions and to establish behavior of unknown contact stresses at the ends of elastic inclusion. In some case using the method of orthogonal polynomials we obtain the dual infinite system of linear algebraic equations. We can manage to investigate the obtained system on the quasi‐regularity and the method of reduction for approximate solution is developed.
National Diet and Nutrition Survey: fat and fatty acid intake from the first year of the rolling programme and comparison with previous surveys
Authors: Pot Gerda K. , Prynne Celia J. , Roberts Caireen , Olson Ashley , Nicholson Sonja K. , Whitton Clare , Teucher Birgit , Bates Beverley , Henderson Helen , Pigott Sarah , Swan Gillian , Stephen Alison M.
Published: July 2011

High saturated fat intake is an established risk factor for several chronic diseases. The objective of the present study is to report dietary intakes and main food sources of fat and fatty acids (FA) from the first year of the National Diet and Nutrition Survey (NDNS) rolling programme in the UK. Dietary data were collected using 4 d estimated food diaries (n896) and compared with dietary reference values (DRV) and previous NDNS results. Total fat provided 34–36 % food energy (FE) across all age groups, which was similar to previous surveys for adults. Men (19–64 years) and older girls (11–18 years) had mean intakes just above the DRV, while all other groups had mean total fat intakes of < 35 % FE. SFA intakes were lower compared with previous surveys, ranging from 13 to 15 % FE, but still above the DRV. Mean MUFA intakes were 12·5 % FE for adults and children aged 4–18 years and all were below the DRV. Meann-3 PUFA intake represented 0·7–1·1 % FE. Compared with previous survey data, the direction of change forn-3 PUFA was upwards for all age groups, although the differences in absolute terms were very small.Trans-FA intakes were lower than in previous NDNS and were less than 2 g/d for all age groups, representing 0·8 % FE and lower than the DRV in all age groups. In conclusion, dietary intake of fat and FA is moving towards recommended levels for the UK population. However, there remains room for considerable further improvement.
Prebiotic fibres dose-dependently increase satiety hormones and alter Bacteroidetes and Firmicutes in lean and obese JCR:LA-cp rats
Authors: Parnell Jill A. , Reimer Raylene A.
Published: July 2011

There is a growing interest in modulating gut microbiota with diet in the context of obesity. The purpose of the present study was to evaluate the dose-dependent effects of prebiotics (inulin and oligofructose) on gut satiety hormones, energy expenditure, gastric emptying and gut microbiota. Male lean and obese JCR:LA-cp rats were randomised to either of the following: lean 0 % fibre (LC), lean 10 % fibre (LF), lean 20 % fibre (LHF), obese 0 % fibre (OC), obese 10 % fibre (OF) or obese 20 % fibre (OHF). Body composition, gastric emptying, energy expenditure, plasma satiety hormone concentrations and gut microbiota (using quantitative PCR) were measured. Caecal proglucagon and peptide YY mRNA levels were up-regulated 2-fold in the LF, OF and OHF groups and 3-fold in the LHF group. GhrelinO-acyltransferase mRNA levels were higher in obesev.lean rats and decreased in the OHF group. Plasma ghrelin response was attenuated in the LHF group. Microbial species measured in the Bacteroidetes division decreased, whereas those in the Firmicutes increased in obesev.lean rats and improved with prebiotic intake.BifidobacteriumandLactobacillusincreased in the OHFv.OC group.Bacteroidesand total bacteria negatively correlated with percentage of body fat and body weight. Enterobacteriaceae increased in conjunction with glucose area under the curve (AUC) and glucagon-like peptide-1 AUC.Bacteroidesand total bacteria correlated positively with ghrelin AUC yet negatively with insulin AUC and energy intake (P < 0·05). Several of the mechanisms through which prebiotics act (food intake, satiety hormones and alterations in gut microbiota) are regulated in a dose-dependent manner. The combined effects of prebiotics may have therapeutic potential for obesity.
Hybridization experiments indicate incomplete reproductive isolating mechanism between Fasciola hepatica and Fasciola gigantica
Authors: ITAGAKI T. , ICHINOMIYA M. , FUKUDA K. , FUSYUKU S. , CARMONA C.
Published: July 2011

Experiments on hybridization between Fasciola hepatica and Fasciola gigantica were carried out to clarify whether a reproductive isolating mechanism appears between the two Fasciola species. Molecular evidence for hybridization was based on the DNA sequence of the internal transcribed spacer 1 (ITS1) region in nuclear ribosomal DNA, which differs between the species. The results suggested that there were not pre-mating but post-mating isolating mechanisms between the two species. However, viable adults of the hybrids F1 and F2 were produced from both parental F. hepatica and F. gigantica. The hybrids inherited phenotypic characteristics such as ratio of body length and width and infectivity to rats from parental Fasciola hepatica and F. gigantica. These findings suggest that reproductive isolation is incomplete between Fasciola hepatica and F. gigantica. Adults of the hybrids F1 and F2 were completely different in mode of reproduction from aspermic Fasciola forms that occur in Asia and seem to be offspring originated from hybridization between F. hepatica and F. gigantica and to reproduce parthenogenetically.
Barriers to the Supply of Non-Government Disability Services in China
Authors: FISHER KAREN R. , LI JING , FAN LEI
Published: July 2011

In the last five years, the Chinese government has begun to encourage the development of non-government organisations (NGO) to increase the supply of social support. Although changes in the NGO sector in China are well researched, questions remain about the barriers to increasing the supply of social services from registered NGOs. We use Mattei's managerial and democratic accountability framework to examine empirical data about the relationship between the way NGO disability services in Beijing are organised and barriers to improving the type, quantity and quality of their social services. Barriers include limited NGO management capacity and underdeveloped government relations. When viewed through the multidimensional accountability framework, the barriers are not surprising. The NGOs' understanding and application of accountability processes are rudimentary. We conclude that government policy to encourage the development of accountability practices of NGOs in China will be critical if it needs NGOs to supply quality social services.
USA300 methicillin-resistant S. aureus (USA300 MRSA) colonization and the risk of MRSA infection in residents of extended-care facilities
Authors: SHURLAND S. M. , STINE O. C. , VENEZIA R. A. , ZHAN M. , FURUNO J. P. , MILLER R. R. , ROGHMANN M.-C.
Published: July 2011

To examine the pathogenesis of USA300 MRSA infection in long-term care residents, we performed a retrospective cohort study of 1691 adult residents of two extended-care facilities from 2003 to 2007 to assess whether the risk of subsequent MRSA infection is higher in USA300 MRSA-colonized residents compared to non-colonized residents or non-USA300 MRSA colonized residents. Six per cent of residents were colonized with USA300 MRSA; 12% of residents were colonized with non-USA300 MRSA; and 101 residents developed MRSA infection. The risk of infection was twofold higher in residents colonized with USA300 MRSA compared to residents not colonized with MRSA [adjusted hazard ratio 2·3, 95% confidence interval (CI) 1·1–4·5]. The risk of infection in USA300 MRSA-colonized residents was similar to USA300 MRSA non-colonized residents (relative risk 1·1, 95% CI 0·5–2·3). Our findings show that colonization with USA300 MRSA increases the risk of MRSA infection suggesting a similar pathogenesis.
Assessing preferential flow through an unsaturated waste rock pile using spectral analysis
Authors: Trinchero Paolo , Beckie Roger , Sanchez‐Vila Xavier , Nichol Craig
Published: July 2011

Waste rock piles are an outcome of open pit and underground mining operations. Unprocessed low‐grade rock is disposed of in piles from several meters high to 100 m+ high. Waste rock piles may still contain sufficient concentrations of metals to be a potential source of pollution. The evaluation of the potential risk involves properly characterizing flow through these piles under unsaturated conditions. The main flow characteristic of the piles is the presence of a large range of grain and pore sizes. Based on data from an instrumented rock pile located in Saskatchewan Canada, unsaturated flow through the pile is modeled as a linear system after separating a fast and a slow component. Water reaching the base of the pile is monitored by 16 contiguous zero‐tension lysimeters. The fast component, flowing through macropores, is assumed to be released instantaneously, while the slow component is simulated using a linear‐reservoir model that assumes the presence of an interconnected porous matrix. An empirical transfer function (TF) is computed as the ratio of the spectra of signals between the output (basal outflow) and the input (rainfall time series). Determination of a parametric transfer function model provides information on the characteristic time of water storage in the matrix and on the fraction of the water within each subsection of the experimental pile that is channeled through the macropores. An analysis of the output signal at different support scales is performed, indicating the nonlinearity of the macropore fraction scaling processes.
Continuity of ocean color data record at risk, according to U.S. National Research Council report
Authors: Showstack Randy
Published: July 2011

Satellite remote sensing of ocean color is important for a number of research and operational uses, including detecting the impacts of climate change on primary productivity; assisting with fisheries and ecosystem‐based management; understanding the optical environment of coastal waters for the operation of ships, submarines, and divers; and monitoring oil spills. However, according to a U.S. National Research Council (NRC) report released on 7 July, U.S. access to the continuous ocean color data record collected by satellites currently is “at risk.” The report, Assessing Requirements for Sustained Ocean Color Research and Operations, calls for several measures to limit or eliminate a potential interruption in the ocean color record, which “would severely hamper the work of climate scientists, fisheries and coastal resource managers, and an expanding array of other users, from the military to oil spill responders.”
Fate of James Webb Space Telescope murky
Authors: Showstack Randy
Published: July 2011

The James Webb Space Telescope (JWST), the next‐generation successor to the Hubble Space Telescope, was put on the chopping block by the U.S. House of Representatives Appropriations Subcommittee on Commerce, Justice, Science, and Related Agencies. The subcommittee approved a measure on 7 July that “terminates funding for [JWST], which is billions of dollars over budget and plagued by poor management.” Then, on 13 July, Rep. Adam Schiff (D‐Calif.), whose district includes NASA's Jet Propulsion Laboratory, tried to insert a funding amendment—transferring $200 million from NASA's Cross‐Agency Support budget to JWST—when the full House Committee on Appropriations voted. That amendment failed in a voice vote.
Variant calling comparison CASAVA1.8 and GATK
Authors: Bauer Denis
Published: July 2011

This work aims at addressing the question of whether the new CASAVA1.8, which boasts improvements such as local realignments of reads, is at par with the well accepted pipeline of BWA mapping, duplicate removal, local realignment, re-calibration and variant calling using GATK. We therefore compare the two methods on chromosome 21 of a Yoruba trio and compare the results to the genotype identified by the 1000 genomes project.We find that the mapping performance is the same for CASAVA1.8 and the academic pipeline, resulting in a mean coverage of about 22. CASAVA1.8 and GATK both call about 70.000 SNPs per individual of which 80% overlap between CASAVA1.8, GATK and the 1000 genomes project. This stands in contrast to the indel calling performance where CASAVA1.8 calls about 12,000 indels while GATK calls 16,000. Furthermore, CASAVA1.8 has a higher Mendelian error rate and frequently more than one alternative allele per locus indicating a non-optimal alignment.We conclude that CASAVA1.8 has come a long way and can be considered a mature SNP calling approach. However, CASAVA1.8 does not deliver the same quality in the indel calling set compared to the newly incorporated Dindel-algorithm of GATK. It hence remains the best practice to use CASAVA1.8 for producing fastq files and switch at this stage to the academic tools for mapping, alignment improvement and variant calling.
In-silico Predictive Mutagenicity Model Generation Using Supervised Learning Approaches
Authors: Passi Anurag , Seal Abhik ,   OSDD Consortium, Jaleel UC Abdul
Published: July 2011

With the advent of High Throughput Screening techniques, it is feasible to filter possible leads from a mammoth chemical space that can act against a particular target and inhibit its action. Virtual screening complements the in-vitro assays which are costly and time consuming. This process is used to sort biologically active molecules by utilizing the structural and chemical information of the compounds and the target proteins in order to screen potential hits. Various data mining and machine learning tools utilize Molecular Descriptors through the knowledge discovery process using classifier algorithms that classify the potentially active hits for the drug development process.
OntoCAT - an integrated programming toolkit for common ontology application tasks
Authors: Adamusiak Tomasz , Kurbatova Natalja , Swertz Morris , Parkinson Helen
Published: July 2011

OntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies.
Response to “Comment on ‘Terahertz wave generation by upper hybrid wave’” [Phys. Plasmas 18, 074701 (2011)]
Authors: Singh Monika , Kumar Sanjay , Sharma R. P.
Published: July 2011

The comment by Stenflo and Brodin mentions two points in our recently published paper [M. Singh, S. Kumar, and R. P. Sharma, Phys. Plasmas 18, 022304 (2011)]. We have given the appropriate reply for the same here.
Nonlinear stationary ac response of the magnetization of uniaxial superparamagnetic nanoparticles
Authors: Mrabti Halim El , Titov Serguey V. , Déjardin Pierre-Michel , Kalmykov Yuri P.
Published: July 2011

The nonlinear stationary ac response of the magnetization of assemblies consisting of (i) noninteracting uniaxial superparamagnetic nanoparticles with aligned easy axes and (ii) randomly oriented nanoparticles subjected to superimposed ac and dc bias magnetic fields of arbitrary strength and orientation is calculated by averaging Gilbert’s equation augmented by a random field. The magnetization dynamics of uniaxial particles driven by a strong ac field applied at an angle to the easy axis of the particle (so that the axial symmetry is broken) alters drastically leading to new nonlinear effects due to coupling of the thermally activated magnetization reversal mode with the precessional modes via the driving ac field. In particular, the high frequency response reveals significant nonlinear effects in the precessional motion with significant consequences for the dynamic hysteresis and ultra-fast switching of the magnetization following an ultrafast change in the applied field.
Nanocrystalline ruthenium oxide embedded zirconium-doped hafnium oxide high-k nonvolatile memories
Authors: Lin Chen-Han , Kuo Yue
Published: July 2011

Metal–oxide–semiconductor capacitors made of the nanocrystalline ruthenium oxide embedded Zr-doped HfO2 high-k film have been fabricated and investigated for the nonvolatile memory properties. Discrete crystalline ruthenium oxide nanodots were formed within the amorphous high-k film after the 950 °C postdeposition annealing step. The capacitor with the Zr-doped HfO2 high-k gate dielectric layer traps a negligible amount of charges. However, with the nanocrystalline ruthenium oxide dots embedded in the high-k film, the capacitor has a large memory window. The charge trapping capacity and the trapping site were investigated using the constant voltage stress method and the frequency-dependent capacitance–voltage measurement. The memory function is mainly contributed by the hole-trapping mechanism. Although both holes and electrons were deeply trapped to the bulk nanocrystalline RuO site, some holes were loosely trapped at the nanocrystal/high-k interface. The current–voltage and charge retention results confirmed the above-mentioned charge trapping mechanism. In summary, this kind of nanocrystal-embedded high-k dielectric has a long charge retention lifetime, which is suitable for future nanosize nonvolatile memory applications.