bluuebunny/crossref_metadata_2025 huggingface dataset:
On the use of the extreme dependency score to investigate the performance of an NWP model for rare events
Authors: Ghelli Anna , Primo Cristina
Published: June 2009

The extreme dependency score (EDS) has been recently proposed as a non‐vanishing measure of skill to verify predictions of rare events. An idealized example is employed to investigate the properties of the EDS when the probability of the event happening is small, as is the case for rare events. The paper warns about the non‐dependency of EDS on the false alarms and the correct rejections when the sample size is fixed, which encourages hedging. Thus, the EDS should not be the sole score used to assess a model's performance on forecasting rare events. The dependency of the EDS on the event probability (base rate) is also analysed. It is shown that the EDS can be written as a function of the base rate and the hit rate, and that only in a very particular condition the score is independent of the event probability. Therefore, when comparing forecasts skills in terms of the EDS, special attention has to be paid to separate the variations in skill from the variations of the probability that the event happens over time.

The score is used to assess the performance of the ECMWF deterministic precipitation forecast over Europe for different forecast ranges and precipitation thresholds. Verification of precipitation forecasts in terms of EDS, combined with an assessment of the false alarm rate, shows a clear improvement of the ECMWF deterministic forecast for precipitation of rare events (i.e. large rainfall amounts). Copyright © 2009 Royal Meteorological Society
NMR‐based metabolomics of urine for the atherosclerotic mouse model using apolipoprotein‐E deficient mice
Authors: Leo Gregory C. , Darrow Andrew L.
Published: June 2009

NMR‐based metabolomics of mouse urine was used in conjunction with the traditional staining and imaging of aortas for the characterization of disease advancement, that is, plaque formation in untreated and drug‐treated apolipoprotein‐E (apoE) knockout mice. The metabolomics approach with multivariate analysis was able to differentiate the captopril‐treated from the untreated mice in general agreement with the staining results. Principal component analysis showed a pattern shift in both the drug‐treated and untreated samples as a function of time that could possibly be explained as the effect of aging. Allantoin, a marker attributed to captopril treatment was elevated in the drug‐treated mice. From partial least squares–discriminant analysis, xanthine and ascorbate were elevated in the untreated mice and were possible markers of plaque formation in the apoE knockout mice. Several additional peaks in the spectra characterizing the study endpoint were found but their respective metabolite identities were unknown. Copyright © 2009 John Wiley & Sons, Ltd.
HongrES1, a cauda epididymis‐specific protein, is involved in capacitation of guinea pig sperm
Authors: Ni Ya , Zhou Yuchuan , Chen Wen‐Ying , Zheng Min , Yu Jianmin , Li Chuyan , Zhang Yonglian , Shi Qi‐Xian
Published: June 2009

Capacitation requires removal of proteins secreted by the cauda epididymis. Previously, we isolated and cloned the HongrES1 gene from rat cauda epididymis and found that it was exclusively expressed there. Here we report that HongrES1 mRNA is also expressed in the guinea pig cauda epididymis using Northern blot analysis, and the molecular weight of its cognate protein is approximately 48 kDa by Western blot analysis. Therefore, we investigated whether HongrES1 was involved in regulation of sperm capacitation in guinea pig. The results show that HongrES1 antisera (HA) significantly enhances sperm capacitation with maximal stimulation at a dilution of 1:500. Capacitation was reversed when capacitated spermatozoa were re‐exposed to HongrES1 protein (HP, 0.25 µg/ml). In other words, HP acted as a decapacitation factor. HA accelerated the onset of capacitation and promoted a sperm hyperactivated motility response. Sperm capacitation was accelerated by HA stimulation of extracellular calcium influx while HP prevented extracellular calcium from influxing. Indirect immunofluorescence staining finds HP localized over the acrosomal anterior region of the sperm head, which exfoliates gradually during capacitation incubation, and completely disappeared after the acrosome reaction. Thus, HongrES1 expressed by the cauda epididymis is a novel molecule that regulates the physiology of guinea pig sperm prior to fertilization. Mol. Reprod. Dev. 76: 984–993, 2009. © 2009 Wiley‐Liss, Inc.
Diverse functions of HBEGF during pregnancy
Authors: Jessmon Philip , Leach Richard E. , Armant D. Randall
Published: June 2009

The establishment of pregnancy requires an intimate physical interaction and a molecular dialogue between the conceptus and the maternal reproductive tract that commences at implantation and continues until the placenta is formed and fully functional. Failure of the regulatory processes that ensure the fidelity of this relationship can precipitate a catastrophic pregnancy loss. One of the earliest identified molecular mediators of blastocyst implantation is heparin‐binding epidermal growth factor (EGF)‐like growth factor (HBEGF), which signals between the endometrium and implanting trophoblast cells to synchronize their corresponding developmental programs. HBEGF expression by trophoblast cells of the developing placenta appears to regulate extravillous differentiation and provide cytoprotection in a sometimes‐hostile environment. This versatile member of the EGF signaling system will be examined in light of its associations with key events during early pregnancy. Mol. Reprod. Dev. 76: 1116–1127, 2009. © 2009 Wiley‐Liss, Inc.
Ion current activity and molecules modulating maturation and growth stages of ascidian (Ciona intestinalis) oocytes
Authors: Silvestre Francesco , Cuomo Annunziata , Tosti Elisabetta
Published: June 2009

Electrophysiological techniques were used to study ion currents in the ascidian Ciona intestinalis oocyte plasma membranes during different stages of growth and meiosis. Three stages (A, B, C) of immature oocytes were discriminated in the ovary, with the germinal vesicle (GV) showing specific different features of growth and maturation. Stage A (pre‐vitellogenic) oocytes exhibited the highest L‐type Ca2+current activity, and were incompetent for meiosis resumption. Stage B (vitellogenic) oocytes showed Na+ currents that remained high during the maturation, up to the post‐vitellogenic stage C oocytes. The latter had acquired meiotic competence, undergoing spontaneous maturation and interacting with the spermatozoon. However, fertilized oocytes did not produce normal larvae, suggesting that cytoplasmic maturation plays a specific role in embryo development. Spontaneous maturation was inhibited at low pH whereas trypsin was able to trigger germinal vesicle breakdown (GVBD) regardless of pH; in addition spontaneous maturation was not affected by removal of follicle cells or by inhibiting junctional communication between oocyte and follicle cells. Taken together these results imply: (i) Ca2+ and Na+ currents are involved in meiotic progression, growth, and acquisition of meiotic competence; (ii) trypsin‐like molecules may have a role as candidates for providing the physiological stimulus to resume meiosis. Finally, we provide evidence that follicle cells in Ciona are not involved in triggering GVBD as it occurs in other ascidians. Mol. Reprod. Dev. 76: 1084–1093, 2009. © 2009 Wiley‐Liss, Inc.
Efficient modal analysis of systems with local stiffness uncertainties
Authors: Wojtkiewicz S. F. , Gaurav
Published: June 2009

The characterization of the uncertainty in modal quantities of an uncertain linear structural system is essential to the rapid determination of its response to arbitrary loadings. Although the size of many computational structural models used is extremely large, i.e. thousands of equations, the uncertainty to be analyzed is oftentimes localized to very small regions of the model. This paper addresses the development of an efficient, computational methodology for the modal analysis of linear structural systems with local stiffness uncertainties. The newly developed methodology utilizes an enriched basis that consists of the sub‐spectrum of a nominal structural system augmented with additional basis vectors generated from a knowledge of the structure of the stiffness uncertainty. In addition, methods for determining bounds on the approximate modal frequencies and mode shapes are discussed. Numerical results demonstrate that the algorithm produces highly accurate results with greatly reduced computational effort. Copyright © 2009 John Wiley & Sons, Ltd.
A quadratic equal‐order stabilized method for Stokes problem based on two local Gauss integrations
Authors: Zheng Haibiao , Shan Li , Hou Yanren
Published: June 2009

In this article, we analyze a quadratic equal‐order stabilized finite element approximation for the incompressible Stokes equations based on two local Gauss integrations. Our method only offsets the discrete pressure gradient space by the residual of the simple and symmetry term at element level to circumvent the inf‐sup condition. And this method does not require specification of a stabilization parameter, and always leads to a symmetric linear system. Furthermore, this method is unconditionally stable, and can be implemented at the element level with minimal additional cost. Finally, we give some numerical simulations to show good stability and accuracy properties of the method. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Single‐cell compact finite‐difference discretization of order two and four for multidimensional triharmonic problems
Authors: Mohanty R.K.
Published: June 2009

In this article, we discuss finite‐difference methods of order two and four for the solution of two‐and three‐dimensional triharmonic equations, where the values of u,(∂2u/∂n2) and (∂4u/∂n4) are prescribed on the boundary. For 2D case, we use 9‐ and for 3D case, we use 19‐ uniform grid points and a single computational cell. We introduce new ideas to handle the boundary conditions and do not require to discretize the boundary conditions at the boundary. The Laplacian and the biharmonic of the solution are obtained as byproduct of the methods. The resulting matrix system is solved by using the appropriate block iterative methods. Computational results are provided to demonstrate the fourth‐order accuracy of the proposed methods. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Maternal plasma pentraxin 3 at 11 to 13 weeks of gestation in hypertensive disorders of pregnancy
Authors: Akolekar Ranjit , Casagrandi Davide , Livanos Panagiotis , Tetteh Amos , Nicolaides Kypros H
Published: June 2009

Objective

To investigate whether in pregnancies that subsequently develop preeclampsia (PE), the maternal plasma concentration of the inflammatory factor pentraxin 3 (PTX3) at 11–13 weeks of gestation is increased and whether such a possible increase is associated with uterine artery pulsatility index (PI).

Methods

The concentration of plasma PTX3 at 11–13 weeks was measured in a case‐control study from 120 pregnancies that developed PE, including 27 who required delivery before 34 weeks (early PE), 87 cases of gestational hypertension (GH) and 207 normal controls. The median PTX3 multiple of the median (MoM) in the control and hypertensive groups were compared. Regression analysis was used to determine the significance of the association between plasma PTX3 and uterine artery PI.

Results

Plasma PTX3 was significantly higher in the early PE group (1.44 MoM; p < 0.0083) but not in late PE (1.11 MoM) or GH (1.10 MoM) compared to the controls (0.97 MoM). There was no significant association between plasma PTX3 levels and uterine artery PI in either the PE group (p = 0.693) or in the controls (p = 0.209).

Conclusion

Increase in maternal plasma PTX3 in pregnancies that subsequently develop early PE is evident from 11–13 weeks but the underlying mechanism for such an increase remains uncertain. Copyright © 2009 John Wiley & Sons, Ltd.
Dispersion, crystallization kinetics, and parameters of Hoffman–Lauritzen theory of polypropylene and nanoscale calcium carbonate composite
Authors: Huang Jiann‐Wen
Published: June 2009

Isothermal and nonisothermal crystallization of polypropylene (PP)/calcium carbonate (CaCO3) with two particle sizes (250–300 nm and 20–25 nm) were studied by differential scanning calorimeter. Equilibrium melting temperature (T) determined from both linear and nonlinear Hoffman–Weeks relations showed that the composites had a lower T as a result of the CaCO3 particles destroying the crystal of PP. Kinetics of the isothermal and nonisothermal crystallization was described by Avrami equation. For the first time, without the assumption of a constant U* value, Lauritzen–Hoffman parameters (U* and Kg) were evaluated directly by data‐fitting method for isothermal crystallization, and by Vyazovkin's method for nonisothermal crystallization. Kg values obtained were similar with and without the assumption of a constant U*and comparable to those in the literature. Both U* and Kg indicate the dual role the CaCO3 particles as nucleating agents to enhance the crystallization and as obstacles to the chain movement to reduce the crystallization. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers
Modeling of the fracture mechanism of HDPE subjected to environmental stress crack resistance test
Authors: Choi Byoung‐Ho , Weinhold Jeffrey , Reuschle David , Kapur Mridula
Published: June 2009

Environmental stress crack resistance (ESCR) is a commonly used test to characterize cracking failure of high‐density polyethylene in applications such as wires, cables, blow molded containers, and other rigid packaging applications. From a resin design standpoint, it is important to understand the mechanism of environmental stress cracking especially in the case of materials with significantly different ESCR values. Currently, two standard ESCR tests, ASTM D1693 and ASTM F2136, are commonly accepted to measure environmental stress crack resistance of HDPE. An accurate observation of ESC is important to understand the fracture mechanism of samples. In this study, the ESCR performance of six HDPE samples was determined per ASTM D1693. The failed specimens were further characterized by scanning electron microscopy and fractographic methodology to investigate the failure mechanism. HDPE resins with low ESCR values had crack surfaces characterized by shorter and fewer fibrils. A new empirical model to predict polymer ESCR using tie chain concentration with different integration range, and water vapor transmission rate, to characterize detergent diffusion in the crack, was developed. The proposed empirical parameter improves the prediction of ESCR. The ability to predict ESCR performance from resin properties is a beneficial tool for new product development. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers
Synthesis and characterization of radio‐opaque thermosensitive poly[N‐isopropylacrylamide‐2,2′‐(ethylenedioxy)bis(ethylamine)‐2,3,5‐triiodobenzamide]
Authors: Leon Christine M , Lee Bae Hoon , Preul Mark , McLemore Ryan , Vernon Brent L
Published: June 2009

BACKGROUND: In situ gelling polymers, like poly(N‐isopropylacrylamide) (poly(NIPAAm)), have many potential medical applications due to their biocompatibility and thermosensitivity.

RESULTS: Radio‐opaque thermosensitive poly(NIPAAm) grafted with 10.7 wt% 2,2′‐(ethylenedioxy)bis(ethylamine)‐2,3,5‐triiodobenzamide was successfully synthesized and characterized. The conjugated polymer showed good visibility with X‐ray fluoroscopy. The polymer had a lower critical solution temperature of 30 °C after conjugation with triiodobenzamide as determined by cloud point determination and a transition peak temperature of 33.3 ± 0.57 °C as determined by differential scanning calorimetry.

CONCLUSION: The polymer synthesized was highly visible under X‐rays, based upon the percentage incorporation of triiodobenzamide. After conjugation of the NIPAAm to the triiodobenzamide through a bis(ethylamine) linkage, the resultant polymer retained lower critical solution temperature characteristics in a temperature region that makes it physiologically useful. Copyright © 2009 Society of Chemical Industry
Enhanced crystallization of the γ‐form of propylene–ethylene copolymer in its miscible blends with propylene homopolymer
Authors: Na Bing , Lv Ruihua , Xu Wenfei , Tian Nana , Li Zhujun , Zhang Zhijie , Fu Qiang
Published: June 2009

BACKGROUND: How to promote the formation of the γ‐form in a certain propylene‐ethylene copolymer (PPR) under atmospheric conditions is significant for theoretical considerations and practical applications. Taking the epitaxial relationship between the α‐form and γ‐form into account, it is expected that incorporation of some extrinsic α‐crystals, developed by propylene homopolymer (PPH), can enhance the crystallization of the γ‐form of the PPR component in PPR/PPH blends.

RESULTS: The PPH component in the blends first crystallizes from the melt, and its melting point and crystal growth rate decrease with increasing PPR fraction. On the other hand, first‐formed α‐crystals of the PPH component can induce the lateral growth of PPR chains on themselves, indicated by sheaf‐like crystal morphology and positive birefringence, which is in turn responsible for enhanced crystallization of the γ‐form of the PPR component.

CONCLUSION: Crystalline/crystalline PPH/PPR blends are miscible and the crystallization of the γ‐form of the PPR component is largely enhanced due to the heterogeneous nucleation from the α‐crystals first developed by the PPH component. Our findings could provide an effective way in practice to obtain isotactic polypropylene copolymers rich in γ‐form. Copyright © 2009 Society of Chemical Industry
Theoretical prediction of size‐expansion effect on the C8‐site activity in the modified guanine‐cytosine analogs
Authors: Li Huifang , Zhang Laibin , Han Li , Cukier Robert I. , Bu Yuxiang
Published: June 2009

Homo/hetero ring‐expanded DNA analogs have been shown to be rationally modified DNA motifs with improved physical or biological properties. In this work, using density functional theory, the stability of these artificial DNA base pairs was examined with regard to three aspects associated with DNA damage, namely deprotonation, H‐abstraction, and H‐radical addition. The effect of size expansion on C8 activity was investigated because C8‐oxidative guanine (G) is one of the most important products of DNA damage. Computational results indicate that the insertion of an aromatic spacer ring in G considerably decreases the electron density over the C8 site, leading to easier deprotonation or H‐abstraction from the C8 site and more difficult H.‐radical attack on the C8 site. However, the opposite phenomenon is observed if the spacer ring is antiaromatic, because of the increased electron density over the C8 site. Moreover, these effects are more prominent the larger the aromaticity or antiaromaticity of the spacer ring. Further analyses, using natural bond orbitals (NBOs) and the nucleus‐independent chemical shift (NICS) index of aromaticity, indicate that the changes of the electron distribution over the C8 site arise because the aromatic spacer ring, involved in the conjugation structure, increases the electron delocalization from the electron‐rich imidazole ring to the diatropic six‐membered rings, while the antiaromatic spacer ring acts as an electron‐donating group, not only inhibiting the above electron delocalization, but also slightly increasing the electron density over the C8 site. The improved stability of these size‐expanded base pairs in different DNA‐damaged environments may encourage their use in practical applications. Copyright © 2009 John Wiley & Sons, Ltd.
Effect of ortho substituents on carbonyl carbon 13C NMR chemical shifts in substituted phenyl benzoates
Authors: Nummert Vilve , Piirsalu Mare , Mäemets Vahur , Vahur Signe , Koppel Ilmar A.
Published: June 2009

13C NMR spectra of 37 ortho‐, meta‐, and para‐substituted phenyl benzoates, containing substituents in benzoyl and phenyl moiety, 4 ortho‐substituted methyl and 5 ethyl benzoates as well as 9 R‐substituted alkyl benzoates have been recorded. The influence of the ortho substituents on the carbonyl carbon 13C NMR chemical shift, δCO, was found to be described by a linear multiple regression equation containing the inductive, σI, resonance, σ°R, and steric, E, or υ substituent constants. For all the ortho‐substituted esters containing substituents in the acyl part as well as the phenyl part, the substituent‐induced reverse inductive effect (ρI < 0), the normal resonance effect (ρR > 0), and the negative steric effect (δortho < 0) with the E were observed. In the case of ortho substituents in the phenyl part, the resonance effect was negligible. Due to inductive effect, the ortho electron‐withdrawing substituents showed an upfield shift or shielding of the carbonyl carbon, while the electron‐donating substituents had an opposite effect. Because of the sterical consequences, ortho substituents revealed a deshielding effect on the 13C NMR chemical shift of the carbonyl carbon. For all the meta‐ and para‐substituted esters, the reverse substituent‐induced inductive and resonance effects (ρI < 0, ρR < 0) were found to be significant. In alkyl benzoates, the alkyl substituents showed the reverse inductive and steric effects. The log k values for the alkaline hydrolysis in water, aqueous 0.5 M Bu4NBr and 2.25 M Bu4NBr, and the IR frequencies, νCO, for the ortho‐, meta‐, and para‐substituted phenyl benzoates and alkyl benzoates were correlated nicely with the corresponding 13C NMR substituent chemical shifts, ΔδCO. Copyright © 2009 John Wiley & Sons, Ltd.
Investigation of sorption phenomena by solid phase extraction and liquid chromatography for the determination of some ether derivatives of tetrabromobisphenol A
Authors: Jonsson Susanne , Hörsing Maritha
Published: June 2009

Observed sorption and chromatographic behaviour served as a starting point for the examination of four ether derivatives of the flame retardant tetrabromobisphenol A (TBBPA): dihydroxyethyl (DHEE), dimethyl (DMe), diallyl (DAE) and dibromopropyl (DBPE). To date, there is little or no information about these compounds in the scientific literature. The targets in the present study had calculated log Kow values of 6.0–10. A broad range of different types of solvents were used in order to elucidate the mechanisms of sorption onto silica (glass) and two solid phase extraction cartridges based on polystyrene divinylbenzene polymers, hydroxylated (Isolute ENV+) and vinylpyrrolidone (Oasis HLB) containing units. Also, three chromatographic columns (C18, C8 and dual C18‐based, i.e. a polar ligand together with C18 on a silica surface) were evaluated. The following were observed: desorption of the targets from silica surface by 1‐propanol showed the best results and the yields were further improved by silylation of the surface. Regardless of the experimental test conditions applied, the lowest recovery was seen for the DMe derivative, followed by TBBPA itself, which had calculated log Kow values in between the other targets. A washing solution containing up to 70% methanol could be used without elution of the targets from the solid phase extraction cartridge . The dihydroxethyl ether derivative of TBBPA is most probably not affected by environmental relevant pH due to a likely high pKa (ca 15). Also, this study shows that the polar character of the dual‐phase column was not as pronounced as asserted by the manufacturer. Copyright © 2009 John Wiley & Sons, Ltd.
Intra‐ and intermolecular NH···O hydrogen bonds in pyrrolyl derivatives of indane‐1,3‐dione – experimental and theoretical study
Authors: Sigalov M. , Shainyan B. , Chipanina N. , Ushakov I. , Shulunova A.
Published: June 2009

2‐(Pyrrol‐2‐ylmethylene)‐1,3‐indandione (4) and 2‐(pyrrol‐2‐ylmethylene)‐3‐dicyanomethylidene‐1‐indanone (5) were synthesized. Multinuclear and 2D‐NMR, IR, UV spectroscopic investigations as well as quantum chemical calculations showed the presence of strong hydrogen bonding in these molecules. For both molecules, the presence of two conformers, with and without H‐bond, was experimentally detected in the basic solvents (DMSO, acetone, pyridine) and the solvate complexes were theoretically calculated. Specific behavior of the intramolecular H‐bonded complexes different from that of the intermolecular H‐complexes is discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Electrochemistry in tetrahydrofuran and at low temperature: protocol, procedures and methods
Authors: Baron Ronan , Kershaw Neil M. , Donohoe Timothy J. , Compton Richard G.
Published: June 2009

This review describes the protocol, procedures and methods for electrochemical studies in THF and at low temperature that have been developed in the course of the last 5 years in our laboratory. Electrochemical studies in THF benefit from a large accessible potential window. In practice, it is however necessary to avoid the presence of humidity in the electrochemical cell. A specific reference electrode had to be designed for those measurements. Microelectrodes, the voltammetric response of which is negligibly affected by the resistivity of the medium, were preferred to macroelectrodes. Moreover, a methodology has been developed for the quantitative analysis of both voltammetric and chronoamperometric curves obtained for the microelectrodes. The fitting of chronoamperometric measurements using the Shoup and Szabo's expression allows us to estimate the diffusion coefficient of the substrate. The modelling of the cyclic voltammograms measured over a large range of scan rates allows the confirmation of the diffusion coefficient of the substrate DA, the determination of the diffusion coefficient of the electrogenerated molecule DB, of the formal potential E, of the transfer coefficient α and of the standard heterogeneous rate constant for the electron transfer k0. Typically, systems are investigated at temperatures ranging from room temperature to 192 K. Parameters obtained at various temperatures are used to extract, through Arrhenius plots, the activation energies both for the diffusion coefficient EA(D) and for the electron transfer reaction EA(k0). Copyright © 2009 John Wiley & Sons, Ltd.
Theoretical calculations of the kinetics and mechanisms of the gas phase elimination of primary, secondary, and tertiary 2‐hydroxyalkylbenzenes
Authors: Mora Jose R. , Lezama Jesus , Albornoz José M. , Hernandez Antonio , Córdova Tania , Chuchani Gabriel
Published: June 2009

Theoretical study of the elimination kinetics of 2‐phenylethanol, 1‐phenyl‐2‐propanol, and 2‐methyl‐1‐phenyl‐2‐propanol in the gas‐phase has been carried out at the MP2/6‐31G(d,p), B3LYP/6‐31G(d,p), B3LYP/6‐31++G(d,p), MPW1PW91/6‐31G(d,p), MPW1PW91/6‐31++G(d,p), PBEPBE/6‐31G(d,p), and PBEPBE/6‐31++G(d,p) levels of theory. The three substrates undergo two parallel elimination reactions. The first elimination appears to proceed through a six‐membered cyclic transition state to give toluene and the corresponding aldehyde or ketone. The second parallel elimination takes place through a four‐membered cyclic transition state producing water and the corresponding unsaturated aromatic hydrocarbon. Results from MP2/6‐31G(d,p) and MPW1PW91/6‐31++G(d,p) methods were found to be in good agreement with the experimental kinetic and thermodynamic parameters in the formation of toluene and the corresponding carbonyl compound. However, the results for PBEPBE/6‐31G(d,p) were in better agreement with the experimental data for the second parallel reaction yielding water and the corresponding unsaturated aromatic hydrocarbon. The charge distribution differences in the TS related to the substitution by methyl groups in the substrates can account for the observed reaction rate coefficients. The synchronicity parameters imply semi‐polar transition states for these elimination reactions. Copyright © 2009 John Wiley & Sons, Ltd.
X‐ray section images of dislocations and dislocation barriers in Si
Authors: Novikov S. , Fodchuk I. , Fedortsov D. , Struk A.
Published: June 2009

By means of numerical solution of the Takagi equations, modeling of X‐ray topographic images of deformation fields of the Lomer–Cottrell dislocation loops and dislocation barriers is made depending on their spatial location for the thin and thick crystals. Diffraction images created by dislocation loops and barriers of different size and spatial location are complicated and versatile in their thin structure.
X‐ray investigation of CdSe nanowires
Authors: Kurtuluş Özgül , Li Zhen , Mews Alf , Pietsch Ullrich
Published: June 2009

CdSe nanowires (NWs) have been prepared by a solution–liquid–solid (SLS) approach using Bi nanocatalysts. Structural characterization has been performed by X‐ray powder diffraction providing an admixture of wurtzite and zinc‐blende (ZB) structure units separated by different types of stacking faults. The relative contributions of ZB type stacking units within the NWs were determined to be in the order of 3–6% from a set of ratios of reflection intensities appearing in only wurtzite structure to those appearing in both ZB and wurtzite (W) structure. In addition, the anisotropy of domain size within the NWs was evaluated from the evolution of peak broadening for increasing scattering length. The coherence lengths along the growth direction are found to be changing between 16 and 21 nm, smaller than the results obtained from TEM measurement, while the NW diameters are determined to be between 5 and 8 nm which is in good agreement with TEM inspection.
A comprehensive investigation of the structural properties of ferroelectric PbZr0.2Ti0.8O3 thin films grown by PLD
Authors: Walker David , Thomas Pam A. , Collins Steve P.
Published: June 2009

X‐Ray diffraction investigations were made of high‐quality epitaxial thin films of the ferroelectric material lead zirconate titanate, PbZr0.2Ti0.8O3 (PZT), grown by pulsed laser deposition (PLD). Layers from 7 to 200 nm in thickness were studied, deposited on a 30 nm SrRuO3 (SRO) electrode on a [001] oriented SrTiO3 (STO) substrate. The out‐of‐plane lattice parameters of the PZT films were measured by high‐resolution X‐ray diffraction using CuKα1 radiation. A significant enhancement of the c lattice parameter with film thickness was observed, the maximum value of 4.25 Å reached in the 30–50 nm thick films. For film thicknesses greater than 100 nm, the c lattice parameter is relaxed, towards the bulk value of 4.13 Å at this composition. The in‐plane lattice parameters were studied by Grazing incidence X‐ray scattering (GIXS), using 15 keV synchrotron radiation at I16, Diamond. The a lattice parameter of domains with [001] oriented normal to the sample surface was effectively lattice matched to the SRO layer in the 7 nm ultra‐thin film, but relaxed compared to the SRO in thicker films. The tetragonality of the [001] oriented domains decreases with increasing film thickness, approaching the bulk value of 1.05 in the thickest films. Evidence for the presence of [100] oriented a‐domains was found in PZT films as thin as 30 nm, the proportion of which increased with increasing film thickness, suggesting they grow in order to relieve stresses that would prevent the epitaxial growth of thicker PZT films. The a‐domains in the thicker films were found to be located nearer to the PZT/SRO interface than to the top surface of the PZT.
Electronic and optical properties of staggered InGaN/InGaN quantum‐well light‐emitting diodes
Authors: Park Seoung‐Hwan , Ahn Doyeol , Koo Bun‐Hei , Kim Jong‐Wook
Published: June 2009

Electronic and optical properties of 440 and 530 nm staggered InGaN/InGaN/GaN quantum‐well (QW) light‐emitting diodes are investigated using the multiband effective‐mass theory. These results are compared with those of conventional InGaN/GaN QW structures. The staggered QW structure requires a slightly larger In composition than the conventional QW structure to obtain a given wavelength. The spontaneous emission is found to be improved with the inclusion of the staggered layer for QW structures with a relatively thick well width and the longer wavelength (λ = 530 nm). On the other hand, in the case of QW structures with a relatively thin well width (Lw = 2 nm), the spontaneous emission peak is almost unaffected by a staggered layer.
Phase transitions and electrical properties of (1−x)(K0.5Na0.5)NbO3−xBiScO3 lead‐free piezoelectric ceramics with a CuO sintering aid
Authors: Li Xuhai , Jiang Meng , Liu Jing , Zhu Jiliang , Zhu Xiaohong , Li Lihua , Zhou Yu , Zhu Jianguo , Xiao Dingquan
Published: June 2009

(1−x)(K0.5Na0.5)NbO3−xBiScO3 doped with 1 mol% CuO (KNN‐BS‐Cu‐x) lead‐free piezoelectric ceramics were prepared by the solid state reaction technique. With the CuO doping, all the ceramics can be well sintered at 1090–1150 °C and exhibit a perovskite structure. After the substitution of BiScO3, the polymorphic phase transition (PPT) was shifted to near room temperature; besides, the cubic–tetragonal phase transitions were also shifted to lower temperatures and a relaxor behavior was induced. The ceramic (x = 0.018) with PPT near room temperature exhibited excellent electrical properties (d33 = 224 pC/N, kp = 0.40, and TC = 331 °C). A relatively high mechanical quality factor (288) was also obtained in this particular composition. All these results reveal that KNN‐BS‐Cu‐x ceramics may become promising candidates for lead‐free piezoelectric materials.
Microwave‐assisted preparation of nanocrystalline ZnS in aqueous solutions of [EMIM][EtSO4] as a low‐cost ionic liquid, and its characterization and photocatalytic properties
Authors: Esmaili M. , Habibi‐Yangjeh A.
Published: June 2009

A fast and template‐free method is proposed for the preparation of nanocrystalline ZnS in the presence of 1‐ethyl‐3‐methylimidazolium ethylsulphate, [EMIM][EtSO4], a room temperature ionic liquid (RTIL), under microwave irradiation for 4 min. Powder X‐ray diffraction (XRD) studies show that the products are excellently crystallized in a cubic structure. Energy dispersive X‐ray (EDX) spectroscopy investigations reveal that the products are extremely pure. The results obtained from scanning electron microscopy (SEM) demonstrate that nanocrystalline ZnS prepared in the presence of the RTIL are smaller than that of the sample prepared in water and the size of the nanoclusters decreases with increasing RTIL content of the media. Diffuse reflectance spectra (DRS) of the as‐prepared ZnS show a blue shift relative to the bulk ZnS, which can be attributed to quantum confinement effect of nanocrystalline ZnS. A possible formation mechanism of the nanocrystalline ZnS in aqueous solutions of the RTIL is presented. The photocatalytic activity of the nanocrystalline ZnS towards photodegradation of methylene blue (MB) was investigated. The results demonstrate that the photocatalytic properties of the nanocrystalline ZnS prepared in the presence of the RTIL are better than that of the sample prepared in water.
Unique structure of ZnO films deposited by chemical bath deposition
Authors: Chu Dewei , Masuda Yoshitake , Kato Kazumi , Hamada Takahiro
Published: June 2009

The unique structure of ZnO films obtained from aqueous solution method was investigated. Scanning electron microscopy (SEM) and X‐ray powder diffraction (XRD) analyses indicate that unique morphology and structure of the region where precipitation on the substrate may occur in parallel with other regions. This is accompanied by a decrease of the electrical resistivity in the absorbed region. A possible mechanism for the resistivity transformation was discussed.
Fast series resistance imaging for silicon solar cells using electroluminescence
Authors: Haunschild Jonas , Glatthaar Markus , Kasemann Martin , Rein Stefan , Weber Eicke R.
Published: June 2009

We introduce a fast and easy to apply method for determining the local series resistance of standard silicon solar cells. For this method only two electroluminescence images taken at different voltages are needed. From these two images, the local voltage and the local current density through the device can be calculated. Knowing these parameters for each pixel yields the local series resistance. By calculating the cell's dark saturation current from the lower voltage image, the method also works with multicrystalline material. We show images, acquired in only 300 ms and compare them with other luminescence based series resistance images. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of metallic coatings on the photoluminescence properties of ZnO nanowires
Authors: Richters J.‐P. , Dev A. , Müller S. , Niepelt R. , Borschel C. , Ronning C. , Voss T.
Published: June 2009

We report on low‐temperature photoluminescence studies of ZnO nanowires coated with thin metallic films. For all analyzed metals (Al, In, Au, Ni, Cu), we find an increased relative intensity of the green deep‐level emission. This is accompanied by a significant reduction of the relative intensity of the surface exciton band. The observed effects are most likely related to the formation of metal induced gap states in the surface region of the ZnO nanowires. A model for the band structure in the surface region of the metal‐coated nanowires is proposed that successfully explains the changes in the photoluminescence spectra after the coating process. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Neuroprotective effect of parthenocissin A, a natural antioxidant and free radical scavenger, in focal cerebral ischemia of rats
Authors: He Shan , Yang Jiehong , Wu Bin , Pan Yuanjiang , Wan Haitong , Wang Yu , Du Yueguang , Wang Shudong
Published: June 2009

Neuroprotective effects of parthenocissin A (PA), a novel antioxidant and free radical scavenger, were studied in a transient middle cerebral artery (MCA) occlusion model in rats for the first time. The animals were treated intraperitoneally with PA at 2.5, 5 or 10 mg/kg, for both 30 min before MCA occlusion and 6 h after reperfusion. The MCA was occluded for 1 h in anesthetized Sprague‐Dawley rats. Compared with vehicle‐treated controls, MCA occluded animals treated with PA showed dose‐dependent reductions in brain infarction size with improved neurological and motor outcome. Biomedical assay showed that the PA treatment suppressed lipid peroxidation and restored superoxide dismutase (SOD) activity in brain tissue. In addition, the ischemia/reperfusion (I/R) induced elevation of nitric oxide (NO) production and nitric oxide synthase (NOS) activity in brain tissue was also inhibited. Thus, PA demonstrated a neuroprotective effect in the I/R model and the beneficial effects of the compound may result from the reduction of oxidative stress and the inhibition of NO production induced by I/R. The neuroprotective effects of PA have highlighted the potential use of stilbene oligomers in stroke therapy. Copyright © 2009 John Wiley & Sons, Ltd.
A Study of CDK2 Inhibitors Using a Novel 3D‐QSAR Method Exploiting Receptor Flexibility
Authors: Mazanetz Michael P. , Withers Ian M. , Laughton Charles A. , Fischer Peter M.
Published: June 2009

A new 3D‐QSAR method based on the novel molecular dynamics methodology, Active Site Pressurization (ASP), has been validated using two cyclin‐dependent kinase 2 data sets containing 65 purines and 91 oxindoles. ASP allows the construction of cavity casts that represent the maximal energetically feasible 3D distortion of protein binding sites potentially achievable by induced fit upon binding of ligands. The ASP‐QSAR method entails many components of traditional 3D‐QSAR strategies but additionally correlates the biological activity of ligand sets with features of ASP‐derived binding site cavity casts, thus taking target protein flexibility into account implicitly. Both of the data sets used to validate the ASP‐QSAR method resulted in QSAR models that were of exceptional quality and predictivity. A non‐cross‐validated variance coefficient (R2) between 0.959 and 0.99 and a cross‐validated variance coefficient (Q2) of between 0.927 and 0.929 were obtained for these ASP‐QSAR models.
QSAR Modeling of 1‐(3,3‐Diphenylpropyl)‐Piperidinyl Amides as CCR5 Modulators Using Multivariate Adaptive Regression Spline and Bayesian Regularized Genetic Neural Networks
Authors: Jalali‐Heravi Mehdi , Mani‐Varnosfaderani Ahmad
Published: June 2009

This study deals with developing a quantitative structure‐activity relationship (QSAR) model for describing and predicting the inhibition activity of 1‐(3,3‐diphenylpropyl)‐piperidinyl derivatives as CCR5 modulators. Applying the multiple linear regressions (MLR) and its inability in predicting the inhibition behavior showed that the interaction has no linear characteristics. To assess the nonlinear characteristics of the inhibition activity artificial neural networks (ANN) was used for data modeling. In order to select the variables needed for developing ANNs, three variable selection algorithms were used: Stepwise‐MLR, genetic algorithm‐partial least squares (GA‐PLS), and Bayesian regularized genetic neural networks (BRGNNs). R2 and root mean square error (RMSE) values for training (t) and leave‐one‐out (LOO) procedures revealed that BRGNNs is a robust algorithm for the variable selection and regression method simultaneously. Due to the ‘black box’ limitation of neural networks, multivariate adaptive regression spline (MARS) technique was used for modeling. A prominent advantage of MARS with respect to ANN is its ability in interpreting of the results of the model. Q2LOO and Rt2 (0.982 and 0.947) reveal that MARS can describe and predict inhibition activity of these modulators and is as robust as ANN. Because the MARS model can explain the activity of molecules, it is a useful model for designing novel CCR5 inhibitors.
Computer‐Aided Prediction of Rodent Carcinogenicity by PASS and CISOC‐PSCT
Authors: Lagunin Alexey , Filimonov Dmitrii , Zakharov Alexey , Xie Wei , Huang Ying , Zhu Fucheng , Shen Tianxiang , Yao Jianhua , Poroikov Vladimir
Published: June 2009

Computer‐aided prediction of rodent carcinogenicity for the external test set consisting of 293 chemicals was performed by PASS (Prediction of Activity Spectra for Substances) and by CISOC‐PSCT. The set included 64 carcinogens from ISS Carcinogens Data Bank and 229 noncarcinogens from the Prestwick Chemical Library. We calculated the accuracy of carcinogenicity prediction by PASS and CISOC‐PSCT in apart, and by the two programs together (the consensus model). Sensitivity, specificity and accuracy (concordance) were calculated for the external test set by PASS (0.81, 0.74, 0.76), by CISOC‐PSCT (0.36, 0.89, 0.77) and by the consensus model (0.69, 0.86, 0.83). Thus, taking into account the prediction results of two computer programs for rodent carcinogenicity the consensus model increases the accuracy of prediction.
Comparative Investigation of the ATP‐Binding Site of Human and Plasmodial Glycogen Synthase Kinase‐3
Authors: Kruggel Sebastian , Lemcke Thomas
Published: June 2009

Malaria is still one of the most problematic infectious diseases besides AIDS and tuberculosis. Plasmodial glycogen synthase kinase‐3 (PfGSK‐3) has been proposed as a potential malaria target before but the plasmodial enzyme is not crystallized yet whereas there are several structures published of the human glycogen synthase kinase‐3 (HsGSK‐3). Here we describe the comparison of different PDB structures of the HsGSK‐3 and corresponding homology models of PfGSK‐3. The differences were investigated with molecular interaction fields and also by a docking study of the known inhibitors kenpaullone and flavopiridol.
Investigating Enzyme Selectivity and Hit Enrichment by Automatically Interfacing Ligand‐ and Structure‐Based Molecular Design
Authors: Nicolotti Orazio , Giangreco Ilenia , Miscioscia Teresa Fabiola , Carotti Angelo
Published: June 2009

A new method was implemented in the in‐house program @lic& to rationally combine structure‐ and ligand‐based design through nondeterministic rescoring of docking poses for the automated generation of structural alignments of a series of benzamidine compounds acting as protease inhibitors. Such alignments enable 3D‐QSAR models to explain enzyme selectivity and to retrieve with high sensitivity active hits from a pool of 260 structurally‐related benzamidine derivatives.
Theoretical study of the Michael addition of acetylacetone to methyl vinyl ketone catalyzed by the ionic liquid 1‐butyl‐3‐methylimidazolium hydroxide
Authors: Wei Xiaofeng , Zhang Dongju , Zhang Changqiao , Liu Chengbu
Published: June 2009

By performing density functional theory calculations, we have investigated the Michael addition of acetylacetone to methyl vinyl ketone in the absence and presence of the ionic liquid 1‐butyl‐3‐methylimidazolium hydroxide ([bmIm]OH). In the absence of ionic liquids, acetylacetone is firstly tautomerized to enol form and then takes place Michael addition to methyl vinyl ketone. As in the catalyzed Michael addition reaction, a bmIm+‐OH− ion pair is introduced into the reaction system to model the effect of the ionic liquid environment on the reactivity. The calculated results show that the anion enhances nucleophilic ability of acetylacetone since the OH− anion captures a proton to form an acetylacetone anion‐H2O complex, and the cation improves the electrophilic ability of methyl vinyl ketone by forming intermolecular hydrogen‐bonds. Both the remarkable effects of the cation and anion on the reactivity of reactants promote this reaction, which take place more easily compared with uncatalyzed reaction. The calculated results show that the main product of the Michael addition is in its ketone form. Our study provides a detailed reaction mechanism of Michael addition catalyzed by basic ionic liquid [bmIm]OH and clearly reveal the catalytic role of ionic liquid in important chemical reaction. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Time‐independent and time‐dependent methods for the calculation of the vibrational spectra: H2CN as example
Authors: Carbonniere Philippe , Pouchan Claude
Published: June 2009

Computed anharmonic transitions and intensities of H2CN are reported in a spectral range ranging from 900 to 2,900 cm−1. Four vibrational treatments were considered from a B3LYP/6‐31+G(d,p) potential electronic surface: The second order perturbational method, the full configuration interaction, the discrete variable representation method and the vibrational analysis arising from a molecular dynamics trajectory. The four approaches yield basically the same results since the convergence of the values is achieved by about 15–20 cm−1. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010