bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the cAMP‐inducible allosteric switch in protein kinase A RIα
Authors: Sjoberg Timothy J. , Kornev Alexandr P. , Taylor Susan S. 
Published: April 2010

AbstractThe regulatory subunits of cAMP‐dependent protein kinase (PKA) are the major receptors of cAMP in most eukaryotic cells. As the cyclic nucleotide binding (CNB) domains release cAMP and bind to the catalytic subunit of PKA, they undergo a major conformational change. The change is mediated by the B/C helix in CNB‐A, which extends into one long helix that now separates the two CNB domains and docks onto the surface of the catalytic subunit. We explore here the role of three key residues on the B/C helix that dock onto the catalytic subunit, Arg226, Leu233, and Met 234. By replacing each residue with Ala, we show that each contributes significantly to creating the R:C interface. By also deleting the second CNB domain (CNB‐B), we show furthermore that CNB‐B is a critical part of the cAMP‐induced conformational switch that dislodges the B/C helix from the surface of the catalytic subunit. Without CNB‐B the Ka for activation by cAMP increases from 80 to 1000 nM. Replacing any of the key interface residues with Ala reduces the Ka to 25–40 nM. Leu233 and M234 contribute to a hydrophobic latch that binds the B/C helix onto the large lobe of the C‐subunit, while Arg226 is part of an electrostatic switch that couples the B/C helix to the phosphate binding cassette where the cAMP docks.
On the fermion spectrum of spontaneously generated fuzzy extra dimensions with fluxes
Authors: Chatzistavrakidis A. , Steinacker H. , Zoupanos G. 
Published: April 2010

AbstractWe consider certain vacua of four‐dimensional SU(N) gauge theory with the same field content as the 𝒩 = 4 supersymmetric Yang‐Mills theory, resulting from potentials which break the 𝒩 = 4 supersymmetry as well as its global SO(6) symmetry down to SO(3) × SO(3). We show that the theory behaves at intermediate scales as Yang‐Mills theory on M4 × SL2 × SR2, where the extra dimensions are fuzzy spheres with magnetic fluxes. We determine in particular the structure of the zero modes due to the fluxes, which leads to low‐energy mirror models.
Photoinduced magnetization of magnetic polarons in Cd0.8Mn0.2Te under high‐density resonant excitation of free exciton
Authors: Katayama K. 
Published: April 2010

AbstractThe pump‐probe Kerr rotation measurement of Cd0.8Mn0.2Te has revealed that the resonant excitation of free excitons is a more suitable method for angular momentum transfer from laser pulse to the exciton magnetic polaron than the band‐to‐band excitation. In the case of band‐to‐band excitation, a formation of macroscopic spin alignment of exciton magnetic polarons is suppressed by heat originating from excess energy of hot electron‐hole pairs and scatterings among the electron‐hole pairs. By contrast, in the case of the resonant excitation, the angular momentum of the laser is transferred to the spins of the exciton magnetic polarons even though the excitation density is higher than the Mott density. These results are consistent and supportive for our suggestion that the selective excitation of localized excitons with energy lower than that of free exciton leads to the high‐spin state of the high‐density exciton magnetic polaron. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interface phonons and polaron effect in II‐VI quantum wells
Authors: Maslov Alexander Yu. , Proshina Olga V. 
Published: April 2010

AbstractThe theory of large radius polaron in II‐VI quantum wells is developed. The analytic expressions for polaron binding energy are obtained for the electron, the hole and the exciton polarons. The numerical results obtained show that the strong electron‐phonon interaction conditions can be realized in the quantum wells based on a number of II‐VI compounds. The influence of the interface optical phonons on the polaron states is accounted for. The extent of interface phonon influence depends on the properties both of the quantum well and of the barrier materials. It is shown that the interaction of charge particles with the interface phonons can lead to the enhancement as well as to the reduction of the polaron effects. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of Shockley‐Read recombination center parameters in MBE p‐Hg1‐xCdxTe/GaAs via photoconductivity in magnetic field
Authors: Protasov D. Yu. , Kostuchenko V. Ya. , Varavin V. S. , Dvoretsky S. A. , Mikhailov N. N. 
Published: April 2010

AbstractA new method for determination of parameters of recombination centres is developed. This method is based on measurements of steady‐state photoconductivity in magnetic field for Faradey's geometry (magnetophotoconductivity). The method was used for investigation of the parameters of recombination centres into MBE p‐HgCdTe with x=0.22. It was obtained, that the energy of recombination centres is lies near to midgap. The ratio between electrons and holes capture coefficients exceeds earlier published data by an order of magnitude. The concentration of recombination centres does not depends on hole concentration in range (4÷8)×1021 m‐3. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
MBE overgrowth of ex‐situ prepared CdSe colloidal nanocrystals
Authors: Rashad M. , Paluga M. , Pawlis A. , Lischka K. , Schikora D. , Artemyev M. V. , Woggon U. 
Published: April 2010

AbstractWe present a growth technique, which combines molecular beam epitaxy of ZnSe and externally wet‐chemically prepared, colloidal NCs of CdSe to achieve fully integrated monolithic epitaxial heterostructures. Our results show that wet‐chemically prepared semiconductor nanocrystals can be incorporated in an epitaxally grown crystalline cap layer. We investigated CdSe core, CdSe/ZnSe and CdSe/ZnS core/shell nanocrystals (NCs) overgrown with cap layers of ZnSe, where the thickness was varied between 20‐40 nm.In this paper we discuss PL measurements of overgrown NCs as a function of the cap layer thickness and compare the results with the PL of NCs in solution. A distinct blue shift of the PL is observed when the core/shell dots are overgrown by ZnSe. We present a model which explains this blue shift as resulting from dissolution of the shell of the dots during the overgrowth (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
ZnSe‐based laser structures for electron‐beam pumping with graded index waveguide
Authors: Gronin S. V. , Sorokin S. V. , Sedova I. V. , Ivanov S. V. , Zdanova E. V. , Zverev M. M. 
Published: April 2010

AbstractElectron beam pumped (EBP) laser heterostructures with graded index waveguide (GIW) have been grown by molecular beam epitaxy and studied in detail. The maximum achieved output pulse power per facet is as high as 8.5 W at an electron beam energy of 16 kV. No saturation of output power with the increase of electron beam current as well as no suitable degradation of GIW EBP laser structures have been observed. The ways for further optimizations of GIW heterostructures are discussed. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Early evolution of the largest‐sized droplets in maritime cumulus clouds
Authors: Lowenstein Jason H. , Blyth Alan M. , Lawson R. Paul 
Published: April 2010

AbstractDroplet size distributions (DSDs) measured within a distance of approximately 1 km above the base of shallow maritime cumulus clouds during the Rain in Cumulus over the Ocean (RICO) field campaign are compared with results of a condensation and stochastic coalescence model, run in the framework of a closed parcel. New measurements of cloud droplets in the critical size range of 30 to 100 µm are presented from the 2D‐S probe. Observations are also presented of the large‐size tail of the sub‐cloud aerosol size distribution measured by the forward‐scattering spectrometer probe. Results show that droplet growth in this region is dominated by condensation, and the large‐size tail of the observed DSDs can be explained with the observed sub‐cloud particles, including giant and ultra‐giant aerosols. Copyright © 2010 Royal Meteorological Society
Science education as a contributor to adequate yearly progress and accountability programs
Authors: Judson Eugene 
Published: April 2010

AbstractThe No Child Left Behind (NCLB) Act requires states to measure the adequate yearly progress (AYP) of each public school and local educational agency (LEA) and to hold schools and LEAs accountable for failing to make AYP. Although it is required that science be assessed in at least three grades, the achievement results from science examinations are not required to be used when calculating AYP. A history of attempts to include science into AYP calculations and the role of science education within state accountability programs is provided here. An examination of National Assessment of Educational Progress science achievement data revealed that those states that opted to make schools accountable for students' science achievement had significantly higher fourth‐grade mean scale scores when compared to states that did not include science in this manner. However, a significant difference was not found between these groups of states when analyzing eighth‐grade data. Specific recommendations are provided to include science into accountability programs and to ameliorate existing requirements of NCLB. © 2010 Wiley Periodicals, Inc. Sci Ed 94:888–902, 2010
Study of the deposition of Ti/TiN multilayers by magnetron sputtering
Authors: Saoula N. , Djerourou S. , Yahiaoui K. , Henda K. , Kesri R. , Erasmus R. M. , Comins J. D. 
Published: April 2010

AbstractIn this study, we present the effect of the plasma deposition parameters on the electrical and structural properties of Ti/TiN multilayers. The films were formed by r.f. magnetron sputtering (13.56 MHz) under nitrogen and argon reactive plasma at low pressure. The first step of our study was the optimization of the deposition conditions in order to obtain good‐quality films. The total pressure was set between 2 and 10 mTorr. The primary result is that the self‐bias voltage plays a major role in the structural evolution of TiN films by changing the preferred film orientation and their hardness. The variation of the resistivity as the function of substrate bias was also investigated. The deposited multilayers were characterized by X‐ray diffraction (XRD), energy dispersive spectroscopy (EDS), and Raman scattering analysis, as well as by the standard four‐probe technique. Copyright © 2010 John Wiley & Sons, Ltd.
Differential toxicity of Disperse Red 1 and Disperse Red 13 in the Ames test, HepG2 cytotoxicity assay, and Daphnia acute toxicity test
Authors: Ferraz E. R. A. , Umbuzeiro G. A. , de‐Almeida G. , Caloto‐Oliveira A. , Chequer F. M. D. , Zanoni M. V. B. , Dorta D. J. , Oliveira D. P. 
Published: April 2010

AbstractAzo dyes are of environmental concern due to their degradation products, widespread use, and low‐removal rate during conventional treatment. Their toxic properties are related to the nature and position of the substituents with respect to the aromatic rings and amino nitrogen atom. The dyes Disperse Red 1 and Disperse Red 13 were tested for Salmonella mutagenicity, cell viability by annexin V, and propidium iodide in HepG2 and by aquatic toxicity assays using daphnids. Both dyes tested positive in the Salmonella assay, and the suggestion was made that these compounds induce mainly frame‐shift mutations and that the enzymes nitroreductase and O‐acetyltransferase play an important role in the observed effect. In addition, it was shown that the presence of the chlorine substituent in Disperse Red 13 decreased the mutagenicity about 14 times when compared with Disperse Red 1, which shows the same structure as Disperse Red 13, but without the chlorine substituent. The presence of this substituent did not cause cytotoxicity in HepG2 cells, but toxicity to the water flea Daphnia similis increased in the presence of the chlorine substituent. These data suggest that the insertion of a chlorine substituent could be an alternative in the design of dyes with low‐mutagenic potency, although the ecotoxicity should be carefully evaluated. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2010.
The cytotoxic effects of synthetic 6‐hydroxylated and 6‐methoxylated polybrominated diphenyl ether 47 (BDE47)
Authors: An Jing , Li Shuhui , Zhong Yufang , Wang Yipei , Zhen Kewen , Zhang Xinyu , Wang Yangjun , Wu Minghong , Yu Zhiqiang , Sheng Guoying , Fu Jiamo , Huang Yuecheng 
Published: April 2010

AbstractPolybrominated diphenyl ethers (PBDE) have been widely applied as flame retardants in plastics, polyurethane foam, paints, and synthetic fabrics. The rising PBDE level in human tissues and environment has led to concern about the health impact of exposure to PBDE. The 2,2′,4,4′‐tetrabromodiphenyl ether (BDE47), the dominant PBDE congener found in the environment and human tissues, has been shown to be an endocrine disruptor. It has also been reported to cause liver and neurodevelopmental toxicity. BDE47 can be metabolized to 6‐OH‐BDE47 and 6‐MeO‐BDE47. So far little has been reported on the cytotoxicity of the metabolites. In the present study, the cytotoxicity of the two metabolites was investigated by exposing human hepatoma cell line HepG2 to different doses of 6‐OH‐BDE47 and 6‐MeO‐BDE47. The cell viability, cell cycle, apoptosis, DNA damage, micronucleus levels, and oxidative stress response were studied. The results indicated that both metabolites could markedly inhibit the proliferation of HepG2 cells with 6‐OH‐BDE47 showing a stronger effect, and significantly increase the micronucleus level and apoptosis rate in a dose‐dependant manner. Moreover, treatment with 6‐OH‐BDE47 (≥0.5 μM) resulted in a marked cell cycle block. The SCGE experiments revealed that both metabolites could cause DNA damage in a dose‐dependant manner. Analysis of the oxidative stress response showed that 6‐OH‐BDE47 treatment (≥2.0 μM) significantly increased intracellular ROS levels as indicated by GSH depletion and elevation of SOD level, whereas 6‐MeO‐BDE47 showed a weaker effect, suggesting that oxidative stress might play a role in the cytotoxic effects. We concluded that 6‐OH‐BDE47 or 6‐MeO‐BDE47 exposure was able to induce inhibition of cell viability, increase of apoptosis rate, cell cycle block, and DNA damages, which might involve the alterated oxidative stress response due to the elevated free radicals and impaired antioxidative system. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Subcellular partitioning links BLM‐based toxicokinetics for assessing cadmium toxicity to rainbow trout
Authors: Liao Chung‐Min , Ju Yun‐Ru , Chen Wei‐Yu 
Published: April 2010

AbstractThe purpose of this article was to develop an integrated‐scale toxicological model to investigate the impact of cadmium (Cd) toxicity on rainbow trout (Oncorhynchus mykiss) based on recent published experimental data. This model was generated from three different types of functional relationship: biotic ligand model (BLM), damage assessment model (DAM), and subcellular partitioning model (SPM), both of key toxicological determinants involved and of functional connections between them. Toxicokinetic parameters of uptake rate constant (k1) and elimination rate constant (k2) in gill, liver, and subcellular fractions were derived. A negative correlation between gill binding fraction of Cd and bioaccumulation factor was found. Detoxifying ability (% detoxified in liver metabolically detoxified pool (MDP)) and k2 were negatively correlated, indicating that increasing % detoxified in MDP can compensate for lower k2. This finding suggests a potential tradeoff between the abilities of elimination and detoxification for Cd. Yet, compensation between the ability to eliminate Cd and the ability to recover Cd‐induced damage was not found. However, changes in k2 and recovery rate constant (kr) can shift the dynamics of Cd susceptibility probability. This analysis implicates that once k2 is determined experimentally, the values of kr and % detoxified in MDP can be predicted by the proposed k2−kr and k2−% detoxified relationships. This study suggests that the mechanistic linking of BLM‐based DAM and SPM can incorporate the organ‐ and cell‐scale exposure experimental data to investigate the mechanisms of ecophysiological response for aquatic organisms exposed to metal stressors. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Effects of 17α‐ethynylestradiol and nonylphenol on liver and gonadal apoptosis and histopathology in Chalcalburnus tarichi
Authors: Kaptaner Burak , Ünal Güler 
Published: April 2010

AbstractChalcalburnus tarichi is an endemic cyprinid fish living in the Lake Van basin located in the Eastern Turkey. Fish (3+ ages) were exposed to 17α‐ethynylestradiol (EE2; 1, 10, 100 ng L−1; nominal concentrations) and nonylphenol (NP; 10, 60, 200 μg L−1; nominal concentrations) for 32 days under semistatic daily renewal conditions. The exposure period was followed by an evaluation of liver and gonadal apoptosis and gonad histopathology in males and females. Exposure to the highest concentrations of EE2 (100 ng L−1) and NP (200 μg L−1) caused significant increases in the extent of apoptosis in liver and gonads. Treatment with 100 ng L−1 of EE2 and 200 μg L−1 NP increased the number of TUNEL positive hepatocytes significantly in both sexes compared to controls. The rates of apoptosis in testicular germ cells and ovarian follicular cells were significantly greater at the same concentrations. Exposure to EE2 (100 ng L−1) and NP (60 and 200 μg L−1) caused thickening of interstitial connective tissue (fibrosis) in the seminiferous tubule wall and testis‐ova formation in males. In females treated with 100 ng L−1 EE2, increased percentage of atretic ooctytes and fibrotic areas in the ovarian somatic stromal tissue were found in the ovaries. Increase in atresia, without a statistical significance, and fibrotic stromal tissue were also noted in 60 and 200 μg L−1 NP treatments. Results suggest that EE2‐ and NP‐dependent hepatotoxicity and gonadotoxicity are causally related to the increase in apoptosis in C. tarichi. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Analytical modeling and resource planning for cognitive radio systems
Authors: Cavdar Derya , Yilmaz H. Birkan , Tugcu Tuna , Alagöz Fatih 
Published: April 2010

AbstractCognitive radio heralds the next step in the evolution of wireless communications. In this paper, an analytical model for infrastructure based cognitive radio systems is proposed, and its performance is evaluated under bursty traffic scenarios in a multiple cell environment. Performance metrics like probabilities of dropping and blocking for primary and secondary users as well as forced termination and forced frequency handoff for secondary users are investigated, and the analytical model is verified with simulations. In addition to the analytical model, a new resource planning method is proposed to compensate for uneven traffic load distribution. The proposed method considers offered traffic, hop count to the heavily loaded cell, and velocity of mobile users during resource planning and performs better in terms of probability of blocking, dropping, and forced termination. The proposed method is promising in balancing the system performance measures, yet there is room for further improvement for finding a closed formula for the proposed analytical model. Copyright © 2010 John Wiley & Sons, Ltd.
Building a push-button RESOLVE verifier: Progress and challenges
Authors: Sitaraman Murali , Adcock Bruce , Avigad Jeremy , Bronish Derek , Bucci Paolo , Frazier David , Friedman Harvey M. , Harton Heather , Heym Wayne , Kirschenbaum Jason , Krone Joan , Smith Hampton , Weide Bruce W. 
Published: April 2010

Abstract
A central objective of the verifying compiler grand challenge is to develop a push-button verifier that generates proofs of correctness in a syntax-driven fashion similar to the way an ordinary compiler generates machine code. The software developer’s role is then to provide suitable specifications and annotated code, but otherwise to have no direct involvement in the verification step. However, the general mathematical developments and results upon which software correctness is based may be established through a separate formal proof process in which proofs might be mechanically checked, but not necessarily automatically generated. While many ideas that could conceivably form the basis for software verification have been known “in principle” for decades, and several tools to support an aspect of verification have been devised, practical fully automated verification of full software behavior remains a grand challenge. This paper explains how RESOLVE takes a step towards addressing this challenge by integrating foundational and practical elements of software engineering, programming languages, and mathematical logic into a coherent framework. Current versions of the RESOLVE verifier generate verification conditions (VCs) for the correctness of component-based software in a modular fashion—one component at a time. The VCs are currently verified using automated capabilities of the Isabelle proof assistant, the SMT solver Z3, a minimalist rewrite prover, and some specialized decision procedures. Initial experiments with the tools and further analytic considerations show both the progress that has been made and the challenges that remain.
Expression of MUC5AC, an early marker of pancreatobiliary cancer, is regulated by DNA methylation in the distal promoter region in cancer cells
Authors: Yamada Norishige , Nishida Yukari , Yokoyama Seiya , Tsutsumida Hideaki , Houjou Izumi , Kitamoto Sho , Goto Masamichi , Higashi Michiyo , Yonezawa Suguru 
Published: April 2010

AbstractBackground and purposeHigh de novo expression of MUC5AC (a gastric‐type secreted mucin) is observed in many types of pancreatobiliary neoplasms, including precursor lesions. In this study, we show that the DNA methylation pattern is intimately correlated with MUC5AC expression in ten cancer cell lines (breast, lung, pancreas, and colon).MethodsThe CpG methylation status of theMUC5AC promoter from −3855 to +321 was mapped using MassARRAY analysis, which utilizes base‐specific cleavage of nucleic acids. ChIP assays and micro‐RNA (miRNA) microarray expression profiling were also carried out in both MUC5AC‐positive cells and in those with no or low MUC5AC expression.ResultsIn the distal region from −3718 to −3670 of the promoter, MUC5AC‐negative cancer cells (e.g., MDA‐MB‐453) were highly methylated, whereas MUC5AC‐positive cells (e.g., MCF‐7) had low methylation levels. The modification status of histone H3 lysine 9 (H3‐K9) was also closely related toMUC5AC expression. Expression levels of miRNAs in the cancer cells were not correlated with MUC5AC expression.ConclusionOur results indicate thatMUC5AC is regulated by CpG methylation and histone H3‐K9 modification of theMUC5AC promoter distal region, but not by miRNAs. An understanding of the epigenetic regulation ofMUC5AC may be of importance for the diagnosis of carcinogenic risk in the pancreatobiliary system.