bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fragmentation features of intermolecular cross‐linked peptides using N‐hydroxy‐ succinimide esters by MALDI‐ and ESI‐MS/MS for use in structural proteomics
Authors: Santos Luiz F. A. , Iglesias Amadeu H. , Gozzo Fabio C. 
Published: July 2011

AbstractThe use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.
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

AbstractBACKGROUND: 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

AbstractBACKROUND: 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 parametersCONCLUSION: 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

AbstractDynamic 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

AbstractFew 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

Abstract
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

AbstractTWIST 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

SUMMARYThe 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.
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

AbstractThe 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

AbstractThe 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.
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

AbstractBACKGROUND: 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

AbstractHighly 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 imageThe 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

AbstractIt 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
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

ABSTRACTSeasonal 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

ABSTRACTElectrical 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.