bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical and experimental studies of the diketene system: Product branching decomposition rate constants and energetics of isomers
Authors: Bui Binh , Tsay Ti Jo , Lin M. C. , Melius C. F.
Published: July 2007

The kinetics and mechanism for the thermal decomposition of diketene have been studied in the temperature range 510–603 K using highly diluted mixtures with Ar as a diluent. The concentrations of diketene, ketene, and CO2 were measured by FTIR spectrometry using calibrated standard mixtures. Two reaction channels were identified. The rate constants for the formation of ketene (k1) and CO2 (k2) have been determined and compared with the values predicted by the Rice–Ramsperger–Kassel–Marcus (RRKM) theory for the branching reaction. The first‐order rate constants, k1 (s−1) = 1015.74 ± 0.72 exp(−49.29 (kcal mol−1) (±1.84)/RT) and k2 (s−1) = 1014.65 ± 0.87 exp(−49.01 (kcal mol−1) (±2.22)/RT); the bulk of experimental data agree well with predicted results. The heats of formation of ketene, diketene, cyclobuta‐1,3‐dione, and cyclobuta‐1,2‐dione at 298 K computed from the G2M scheme are −11.1, −45.3, −43.6, and −40.3 kcal mol−1, respectively. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 580–590, 2007
Micellar and salt effects on the interaction of [Cu(II)‐Gly‐Gly]+ with ninhydrin
Authors: Akram Mohd. , Zaidi Neelam Hazoor , Kabir‐ud‐Din
Published: July 2007

The effect of cationic micelles of cetyltrimethylammonium bromide (CTAB) on the kinetics of interaction of copper dipeptide complex [Cu(II)‐Gly‐Gly]+ with ninhydrin has been studied spectrophotometrically at 70°C and pH 5.0. The reaction follows first‐ and fractional‐order kinetics, respectively, in complex and ninhydrin. The reaction is catalyzed by CTAB micelles, and the maximum rate enhancement is about twofold. The results obtained in the micellar medium are treated quantitatively in terms of the kinetic pseudophase and Piszkiewicz models. The rate constants (kobs or kΨ), micellar‐binding constants (kS for [Cu(II)‐Gly‐Gly]+, kN for ninhydrin), and index of cooperativity (n) have been evaluated. A mechanism is proposed in accordance with the experimental results. The influence of different inorganic (NaCl, NaBr, Na2SO4) and organic (NaBenz, NaSal) salts on the reaction rate has also been seen, and it is found that tightly bound/incorporated counterions are the most effective. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 556–564, 2007
Detection of the OH band fine structure in liquid water by means of new treatment procedure based on the statistics of the fractional moments
Authors: Pershin S M , Bunkin A F , Lukyanchenko V A , Nigmatullin R R
Published: July 2007

Three main spectral components ∼ 3210, 3450, and 3650 cm-1separated by deep gaps in the Raman OH band of liquid water have been detected by a new treatment procedure of experimental data. The applied treatment is based on the statistics of the fractional moments. This approach includes the consideration of the total set of the moments (the fractional and even complex ones) and the generalized mean value functions (GMV) as a specific noise ``label''. The possibility of the extraction and quantitative description of the fine structure of the averaging experimental spectra is demonstrated. In the frame of the novel approach the reliable separation between Raman spectra of the distilled and Milli-Q water is obtained.
Regularized meshless method for antiplane shear problems with multiple inclusions
Authors: Chen K. H. , Chen J. T. , Kao J. H.
Published: July 2007

In this paper, we employ the regularized meshless method to solve antiplane shear problems with multiple inclusions. The solution is represented by a distribution of double‐layer potentials. The singularities of kernels are regularized by using a subtracting and adding‐back technique. Therefore, the troublesome singularity in the method of fundamental solutions (MFS) is avoided and the diagonal terms of influence matrices are determined. An inclusion problem is decomposed into two parts: one is the exterior problem for a matrix with holes subjected to remote shear, the other is the interior problem for each inclusion. The two boundary densities, essential and natural data, along the interface between the inclusion and matrix satisfy the continuity and equilibrium conditions. A linear algebraic system
is obtained by matching boundary conditions and interface conditions. Finally, numerical results demonstrate the accuracy of the present solution. Good agreements are obtained and compare well with analytical solutions and Gong's results. Copyright © 2007 John Wiley & Sons, Ltd.
Coupling of a non‐overlapping domain decomposition method for a nodal finite element method with a boundary element method
Authors: Boubendir Y. , Bendali A. , Fares M. B.
Published: July 2007

Non‐overlapping domain decomposition techniques are used to solve the finite element equations and to couple them with a boundary element method. A suitable approach dealing with finite element nodes common to more than two subdomains, the so‐called cross‐points, endows the method with the following advantages. It yields a robust and efficient procedure to solve the equations resulting from the discretization process. Only small size finite element linear systems and a dense linear system related to a simple boundary integral
equation are solved at each iteration and each of them can be solved in a stable way. We also show how to choose the parameter defining the augmented local matrices in order to improve the convergence. Several numerical simulations in 2D and 3D validating the treatment of the cross‐points and illustrating the strategy to accelerate the iterative procedure are presented. Copyright © 2007 John Wiley & Sons, Ltd.
Finite element approximation of a forward and backward anisotropic diffusion model in image denoising and form generalization
Authors: Ebmeyer Carsten , Vogelgesang Jens
Published: July 2007

A new forward–backward anisotropic diffusion model is introduced. The two limit cases are the Perona‐Malik equation and the Total Variation flow model. A fully discrete finite element scheme is studied using C0‐piecewise linear elements in space and the backward Euler difference scheme in time. A priori estimates are proven. Numerical results in image denoising and form generalization are presented.© 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
Computational analysis of human protein interaction networks
Authors: Ramírez Fidel , Schlicker Andreas , Assenov Yassen , Lengauer Thomas , Albrecht Mario
Published: July 2007

Large amounts of human protein interaction data have been produced by experiments and prediction methods. However, the experimental coverage of the human interactome is still low in contrast to predicted data. To gain insight into the value of publicly available human protein network data, we compared predicted datasets, high‐throughput results from yeast two‐hybrid screens, and literature‐curated protein‐protein interactions. This evaluation is not only important for further methodological improvements, but also for increasing the confidence in functional hypotheses derived from predictions. Therefore, we assessed the quality and the potential bias of the different datasets using functional similarity based on the Gene Ontology, structural iPfam domain‐domain interactions, likelihood ratios, and topological network parameters. This analysis revealed major differences between predicted datasets, but some of them also scored at least as high as the experimental ones regarding multiple quality measures. Therefore, since only small pair wise overlap between most datasets is observed, they may be combined to enlarge the available human interactome data. For this purpose, we additionally studied the influence of protein length on data quality and the number of disease proteins covered by each dataset. We could further demonstrate that protein interactions predicted by more than one method achieve an elevated reliability.
Two‐dimensional wavepacket dynamics with quantum hydrodynamics
Authors: Matsumoto D. , Hayashi K. , Ida T. , Mizuno M. , Endo K. , Nishikawa K.
Published: July 2007

Wyatt and coworkers introduced a new approach (Wyatt, Quantum Dynamics with Trajectories Introduction to Quantum Hydrodynamics, Springer, New York, 2005; Lopreore and Wyatt, Phys Rev Lett, 1999, 82, 5190; Wyatt et al., J Chem Phys, 2001, 114, 5113; Lopreore and Wyatt, J Chem Phys, 2002, 116, 1228; Trahan and Wyatt, J Chem Phys, 2003, 118, 4784; Trahan et al., J Chem Phys, 2005, 122, 164104; Babyuk and Wyatt, J Chem Phys, 2006, 125, 64112) which is based on quantum hydrodynamics to the quantum wavepacket dynamics and applied to several systems including tunneling and nonadiabatic transition. This approach is expected to overcome some disadvantages of the conventional wavepacket dynamics, such as order‐N problem and use of absorbing potential. We applied this method to two‐dimensional model of quantum tunneling system and compared the new approach with the conventional wavepacket simulation since the validity of this method to multidimensional systems is not well known. In the simulation, we adopted two different model potentials (Model I and Model II) and calculated time dependence of the probability density and the tunneling probability in both models, where we showed explicitly that the results of the quantum hydrodynamics are identical with those of the conventional method. Using the moving grid and the regridding algorithm in the quantum hydrodynamics, we can effectively avoid order‐N problem and use of the absorbing potential. In addition to these computational advantages, the flux vector is easily obtained by the quantum hydrodynamics and these vectors field helps us to intuitively understand detailed tunneling dynamics. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Simultaneous detection of N‐terminal fragment ions in a protein mixture using a ruthenium(II) complex
Authors: Ito Akihiro , Okamura Taka‐aki , Yamamoto Hitoshi , Ueyama Norikazu , Yamaguchi Minoru , Kuyama Hiroki , Ando Eiji , Tsunasawa Susumu , Ake Kojiro , Masui Ryoji , Kuramitsu Seiki , Nakazawa Takashi , Norioka Shigemi
Published: July 2007

Use of a bis(terpyridine)ruthenium(II) derivative as an N‐terminal labeling reagent resulted in the simultaneous detection and individual determination of all the N‐terminal fragments of the proteins in a mixture without requiring any separation. All of the N‐termini of the guanidinated proteins were labeled selectively by the ruthenium complex (‐CO‐labeling). After chymotryptic digestion, the fragments were analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) and post‐source decay (PSD). The ‐CO moiety exclusively enhanced N‐terminal fragment ions in mass spectra and enabled easy N‐terminal sequencing. In a mixture containing three different proteins (lysozyme, ubiquitin, and insulin), all of the N‐terminal fragment ions labeled with the ruthenium complex were found to produce uniformly intense peaks without the detection of the other unlabeled fragments. The N‐terminal sequences of these ions were determined individually by PSD analysis. Application to unknown proteins from Thermus thermophilus HB8 with two‐dimensional electrophoretic separation resulted in the successful determination of the N‐terminal sequence and easy identification of the target protein. Copyright © 2007 John Wiley & Sons, Ltd.
Quantitative analysis of a proteome by N‐terminal stable‐isotope labelling of tryptic peptides
Authors: Fedjaev Michael , Trudel Stephanie , Tjon‐A‐Pan Natascha , Parmar Amanda , Posner Barry I. , Levy Emile , Nifant'ev Ilya , Pshezhetsky Alexey V.
Published: July 2007

Covalent modification of peptides and proteins with compounds containing stable isotopes (isotope tagging) has become an essential tool to detect dynamic changes in the proteome following external or internal influence; however, using terminal amino groups for global isotope labelling of tryptic peptides is challenged by the similar reactivity of the amino groups of lysine residues. We describe a new quantitative method based on selective tagging of the terminal amino groups of tryptic peptides with pentafluorophenyl esters containing stable isotopes. The labelled peptides were resolved by two‐dimensional nanoflow liquid chromatography on weak anion‐exchange and reversed‐phase columns and then identified and quantified by tandem mass spectrometry. The method was applied to compare the proteomes of plasma membranes from proliferating and differentiated human colorectal adenocarcinoma (Caco‐2) cells and endosomes purified from the livers of rats stimulated with insulin and epidermal growth factor. The comparison of the results obtained by isotope tagging and biochemical assays demonstrate that global isotope tagging with pentafluorophenyl esters allows accurate quantification of complex protein samples. Copyright © 2007 John Wiley & Sons, Ltd.
Creating Nanopatterns of His‐Tagged Proteins on Surfaces by Nanoimprint Lithography Using Specific NiNTA‐Histidine Interactions
Authors: Maury Pascale , Escalante Maryana , Péter Mária , Reinhoudt David N. , Subramaniam Vinod , Huskens Jurriaan
Published: July 2007

Directed assembly of the DsRed FT protein is demonstrated on self‐assembled monolayers (SAMs) on silicon substrates patterned by nanoimprint lithography. Initially, the DsRed protein is attached using electrostatic interactions on both topographical (polymer) templates with an amino functionalization and on chemically patterned (flat) substrates. In a second experiment, a patterned NiNTA SAM is used in order to attach the DsRed FT protein via supramolecular interactions, taking advantage of the histidine functionalization of the DsRed FT protein. The NTA SAM is formed on silicon oxide using a multistep covalent process. Patterning of the NTA SAM is performed using nanoimprint lithography. The DsRed FT protein is attached on the patterned NTA layer after treating this with a NiII solution. Moreover, the histidine‐NiNTA binding may be reversed by removing the Ni using EDTA or by competition using imidazole. The regeneration and reuse of the substrate by subsequently attaching and removing two different histidine‐functionalized proteins from the patterned NTA is shown by fluorescence microscopy.
Oto, a generic and extensible tool for marking programming assignments
Authors: Tremblay G. , Guérin F. , Pons A. , Salah A.
Published: July 2007

Marking programming assignments in programming courses involves a lot of work: each program must be tested, the source code must be read and evaluated, etc. With the large classes encountered nowadays, the feedback provided to students through marking is thus rather limited, and often late. Tools providing support for marking programming assignments do exist, ranging from support for administrative aspects through automation of program testing or support for source code evaluation based on metrics. In this paper, we introduce a tool, called Oto, that provides support for submission and marking of assignments. Oto aims at reducing the workload associated with the marking task. Oto also aims at providing timely feedback to the students, including feedback before the final submission. Furthermore, the tool has been designed to be generic and extensible, so that the marking process for a specific assignment can easily be customized and the tool can be extended with various marking components (modules) that allows it to deal with various aspects of marking (testing, style, structure, etc.) and with programs written in various programming languages. Copyright © 2007 John Wiley & Sons, Ltd.
FIRE/J—optimizing regular expression searches with generative programming
Authors: Karakoidas Vassilios , Spinellis Diomidis
Published: July 2007

Regular expressions are a powerful tool for analyzing and manipulating text. Their theoretical background lies within automata theory and formal languages. The FIRE/J (fast implementation of regular expressions for Java) regular expression library is designed to provide maximum execution speed while remaining portable across different machine architectures. To achieve that, FIRE/J transforms each regular expression into a tailor‐made class file, which is compiled directly to Java virtual machine (JVM) bytecodes. The library is compatible with the POSIX standard. Copyright © 2007 John Wiley & Sons, Ltd.
Chemical Composition and Structure of Granule Periphery and Envelope Remnant of Rice Starches as Revealed by Chemical Surface Gelatinization
Authors: Wang Ya‐Jane , Kuo Meng‐I , Wang Linfeng , Patindol James
Published: July 2007

In this work the contribution of molecular structures to the swelling behavior of rice starches was investigated. Rice starches with different amylose contents (0 ‐ 23.4 %) were gelatinized to various degrees (approximately 10, 20, and 50 %) with 13 M aqueous LiCl, and the surface‐gelatinized starch and ungelatinized remaining granules were separated and characterized. The native starches were heated at 85 or 95°C for 30 min in excess water, and the granule envelope remnants were recovered by centrifugation for further characterization. The remaining granules after surface removal exhibited a lower gelatinization temperature and enthalpy, and swelled to a greater extent upon heating than the native counterpart. The amylopectin molecules in granule envelope remnants obtained at 95°C had larger Mw (weight‐average molar mass) and Rz (z‐average gyration radius) than those in remnants obtained at 85°C. The chemical composition and structure of granule envelope remnants obtained at 85°C were different from those obtained at 95°C for the same rice starch cultivar. The results imply that starch periphery may not be responsible for maintaining starch granule integrity during gelatinization and swelling. It is proposed that the composition and structure of the granule envelope remnant that maintains granule integrity are not constant but dynamic. The formation of a semi‐permeable membrane‐like surface structure during gelatinization and swelling is proposed to be a result of molecule entanglement after gelatinization.
Mechanisms of progression of chronic kidney disease
Authors: Fogo Agnes B.
Published: July 2007

Chronic kidney disease (CKD) occurs in all age groups, including children. Regardless of the underlying cause, CKD is characterized by progressive scarring that ultimately affects all structures of the kidney. The relentless progression of CKD is postulated to result from a self-perpetuating vicious cycle of fibrosis activated after initial injury. We will review possible mechanisms of progressive renal damage, including systemic and glomerular hypertension, various cytokines and growth factors, with special emphasis on the renin–angiotensin–aldosterone system (RAAS), podocyte loss, dyslipidemia and proteinuria. We will also discuss possible specific mechanisms of tubulointerstitial fibrosis that are not dependent on glomerulosclerosis, and possible underlying predispositions for CKD, such as genetic factors and low nephron number.
Interferon‐gamma and lipopolysaccharide stimulation increases matrix metalloproteinase‐9 expression and enhances invasion activity in ras/myc‐transformed serum‐free mouse embryo cells
Authors: Kidachi Yumi , Yamaguchi Hideaki , Umetsu Hironori , Ryoyama Kazuo
Published: July 2007

Ras/myc‐transformed serum‐free mouse embryo (ras/myc SFME) cells were treated with interferon‐gamma (IFN‐γ, 100 units/ml) and/or lipopolysaccharide (LPS, 0.5 μg/ml) for 24 h to investigate the effects of these ligands on the expression of matrix metalloproteinase‐9 (MMP‐9) and tissue inhibitor of metalloproteinase‐1 (TIMP‐1). Aminoguanidine (AG, 1 mM; a nitric oxide synthase [NOS] inhibitor) was also added along with IFN‐γ and LPS to analyze a possible association of NO with invasiveness. Treatment of cells with IFN‐γ alone did not alter MMP‐9 mRNA expression or pro‐MMP‐9 production, but LPS alone and IFN‐γ + LPS co‐treatment enhanced them significantly. TIMP‐1 mRNA expression remained unchanged with or without treatment and the mRNA expression of MMP‐9 exceeded that of TIMP‐1 in LPS‐ or IFN‐γ + LPS‐treated cells. Co‐treatment of cells with IFN‐γ and LPS up‐regulated invasiveness and indicated a possible involvement of NO in the enhancement of invasiveness. These results suggest that ras/myc SFME cells respond to inflammatory and infectious conditions and that they may possibly modulate their characteristics as cancer cells due to their increase in MMP‐9 expression and invasion activity.
Decadal analysis of hydrography and in situ nutrient budgets in the western and eastern North Atlantic subtropical gyre
Authors: Cianca Andrés , Helmke Peer , Mouriño Beatriz , Rueda María José , Llinás Octavio , Neuer Susanne
Published: July 2007

The current debate about the mechanisms and magnitude of new nutrient input to the euphotic zone in subtropical gyres calls for studies which consider large and mesoscale perspectives by combining in situ time series and remote observations. We carried out a first of its kind comparative analysis of hydrography and sea level anomaly (SLA) at the oligotrophic time series stations BATS (Bermuda Atlantic Time Series Study) and ESTOC (European Station for Time Series, Canary Islands) using concomitant 10‐yr in situ and satellite altimetry data. The stations are located at about the same latitude in the western and eastern boundaries of the subtropical North Atlantic gyre, respectively, and provide the opportunity to study differences that may exist between both regions. Observed SLA was 0.25 m at BATS, compared with 0.12 m at ESTOC, a consequence of the higher eddy kinetic energy in the western compared with the eastern subtropical gyre. We quantified a detailed in situ nutrient budget for both time series stations; ESTOC received about 75% of the nutrients available for new production at BATS (in average 0.28 mol N m−2 yr−1 compared with 0.38 mol N m−2 yr−1, respectively), but the difference was not significant. However, significant differences in input mechanisms existed between both stations; eddy pumping constituted the main new nutrient source BATS, whereas wintertime convection was the main nutrient supply mechanism at ESTOC. In addition, the nutricline was significantly shallower at ESTOC compared with BATS, partly compensating for shallower mixed‐layer depths and SLA variability at the western station. We found considerable interannual variability in both eddy pumping and wintertime convection which may be related to NAO‐induced changes in the pattern of the subtropical gyre.
Impact of long‐range correlations on trend detection in total ozone
Authors: Vyushin Dmitry I. , Fioletov Vitali E. , Shepherd Theodore G.
Published: July 2007

Total ozone trends are typically studied using linear regression models that assume a first‐order autoregression of the residuals [so‐called AR(1) models]. We consider total ozone time series over 60°S–60°N from 1979 to 2005 and show that most latitude bands exhibit long‐range correlated (LRC) behavior, meaning that ozone autocorrelation functions decay by a power law rather than exponentially as in AR(1). At such latitudes the uncertainties of total ozone trends are greater than those obtained from AR(1) models and the expected time required to detect ozone recovery correspondingly longer. We find no evidence of LRC behavior in southern middle‐and high‐subpolar latitudes (45°–60°S), where the long‐term ozone decline attributable to anthropogenic chlorine is the greatest. We thus confirm an earlier prediction based on an AR(1) analysis that this region (especially the highest latitudes, and especially the South Atlantic) is the optimal location for the detection of ozone recovery, with a statistically significant ozone increase attributable to chlorine likely to be detectable by the end of the next decade. In northern middle and high latitudes, on the other hand, there is clear evidence of LRC behavior. This increases the uncertainties on the long‐term trend attributable to anthropogenic chlorine by about a factor of 1.5 and lengthens the expected time to detect ozone recovery by a similar amount (from ∼2030 to ∼2045). If the long‐term changes in ozone are instead fit by a piecewise‐linear trend rather than by stratospheric chlorine loading, then the strong decrease of northern middle‐ and high‐latitude ozone during the first half of the 1990s and its subsequent increase in the second half of the 1990s projects more strongly on the trend and makes a smaller contribution to the noise. This both increases the trend and weakens the LRC behavior at these latitudes, to the extent that ozone recovery (according to this model, and in the sense of a statistically significant ozone increase) is already on the verge of being detected. The implications of this rather controversial interpretation are discussed.
Uncertainty and the changing hydroclimatology of the Amazon
Authors: Moore Nathan , Arima Eugenio , Walker Robert , Ramos da Silva Renato
Published: July 2007

Using a spatially‐explicit model, we have projected potential Amazon landscapes based on two possible development scenarios and total forest removal to represent uncertainty in future land cover. We conducted Monte Carlo simulations with a regional climate model driven by these landscapes and by different years to include atmospheric uncertainty. Absent restraints on development, we find that certain areas can expect annual rainfall declines of 3–5% that persist in spite of introduced uncertainty. These declines are strongly tied to key landscape features. Land cover and land use change associated with major roads, not ENSO events or other annual atmospheric features, leads to reduced rainfall. For the case of total deforestation we found an average annual decline in rainfall of 10–20% across the entire basin.
Interhemispheric influence of surface buoyancy conditions on a circumpolar current
Authors: Fučkar Neven S. , Vallis Geoffrey K.
Published: July 2007

This study shows that the surface buoyancy conditions in the Northern Hemisphere may influence the stratification and transport of the Antarctic Circumpolar Current (ACC). We use a course‐resolution ocean general circulation model (OGCM) in an idealized single‐basin configuration with a circumpolar channel. A decrease in the magnitude of the surface temperature meridional gradient in the Northern Hemisphere reduces production of the deep water, affecting the interhemispheric Meridional Overturning Circulation (MOC) and deepening the thermocline in both hemispheres. The induced change of stratification in the Southern Hemisphere circumpolar region increases the zonal volume transport of circumpolar current because of an increase in the local meridional density gradient and the associated thermal wind shear, which is the dominant baroclinic component of the total volume transport. The result is robust to variations in the background vertical mixing and the parameterization scheme for mesoscale eddies.
Systematic anomalies over inland water bodies in satellite‐based precipitation estimates
Authors: Tian Yudong , Peters‐Lidard Christa D.
Published: July 2007

We studied two recent high‐resolution precipitation datasets derived from satellite remote‐sensing, TRMM 3B42 and CMORPH, and compared them with ground‐based radar and gauge measurements in the southeastern U. S. We found there are systematic differences in rainfall estimates between inland water‐body pixels and land pixels. On average, there are about twice as many raining days over water bodies than over land pixels in the satellite products, causing much higher false alarm rates over water bodies. The increased false alarms occur mostly in the form of light rain (<2 mm/day), and lead to significantly different rain rate distributions between water‐body and land pixels. We speculate that this inconsistency is caused by deficiencies in emissivity characterization for the passive microwave‐based rainfall retrievals that serve as input to these merged products.
The peptidase inhibitor CGS‐26303 increases endothelin converting enzyme‐1 expression in endothelial cells through accumulation of big endothelin‐1
Authors: Raoch V , Martinez‐Miguel P , Arribas‐Gomez I , Rodriguez‐Puyol M , Rodriguez‐Puyol D , Lopez‐Ongil S
Published: July 2007

Background and purpose:

CGS‐26303 inhibits endothelin converting enzyme (ECE)‐1 more specifically than phosphoramidon. We have studied the effect of CGS‐26303 on ECE‐1 expression in bovine aortic endothelial cells.

Methods:

ECE‐1 activity and big endothelin (ET)‐1 levels were measured by ELISA, ECE‐1 expression using western and northern blot and promoter activity using transfection assays.

Key results:

ECE‐1 activity was completely inhibited by CGS‐26303 25 μ
M and phosphoramidon 100 μ
M. CGS‐26303 and phosphoramidon, though not thiorphan, a neutral endopeptidase (NEP) inhibitor, stimulated ECE‐1 expression in cells (maximal effect at 16 h, 25 μ
M). Cycloheximide abolished that effect. CGS‐26303 induced ECE‐1 mRNA expression and ECE‐1 promoter activity. CGS‐35066, a selective ECE‐1 inhibitor, mimicked the effects of CGS‐26303, suggesting that the effect was specific to ECE‐1 inhibition. Big ET‐1 accumulated in the cells and in the supernatants after CGS‐26303 treatment. Neither exogenously added ET‐1 nor the blockade of their receptors with bosentan modified ECE‐1 protein. When big ET‐1 was added to cells, significant increases in ECE‐1 protein content and ECE‐1 promoter activity were found. Bosentan did not block those effects. CGS‐26303 did not modify prepro‐ET‐1 expression. CGS‐26303 and big ET‐1 induced the same effects in human endothelial cells, at lower doses.

Conclusions:

These results suggest that the accumulation of big ET‐1 is responsible for the effects of CGS‐26303 on ECE‐1 and they did not depend on NEP blockade. Changes in ECE‐1 protein after the administration of CGS‐26303 could lead to a decreased response in long‐term treatments.

British Journal of Pharmacology (2007) 152, 313–322; doi:10.1038/sj.bjp.0707398; published online 23 July 2007
Immunosuppressive effects of chloroquine: potential effectiveness for treatment of post‐transfusion graft‐versus‐host disease
Authors: Nishimura M. , Hidaka N. , Akaza T. , Tadokoro K. , Juji T.
Published: July 2007

Post‐transfusion graft‐versus‐host disease (PT‐GVHD) is a fatal adverse effect of blood transfusion. In spite of its severity, there is no effective treatment at present for PT‐GVHD. Previously, we reported that chloroquine (CH) inhibited the cytotoxicity of cytotoxic T‐cell (CTL) clones and tumour necrosis factor β (TNF β) production by TNF β‐producing clones in vitro, both the clones being derived from peripheral blood lymphocytes (PBMCs) of PT‐GVHD patients. To explore the possibility of utilizing CH for the treatment of PT‐GVHD, we extended our investigation of the immunosuppressive effects of CH in vitro to PBMCs derived from healthy donors. Our results show that CH inhibits the mixed lymphocyte reaction (MLR) between allogeneic PBMCs, production of inflammatory cytokines such as TNF α, interleukin‐1β (IL‐1β) and interferon γ (IFN γ) in mixed lymphocyte culture and natural killer cell activity, and, further, reduces the number of alloreactive CTL precursors.
Evolution of the porous volume during the aerogel-glass transformation
Authors: WOIGNIER T. , QUINSON J. F. , PAUTHE M. , REPELLIN-LACROIX M. , PHALIPPOU J.
Published: July 2007

The evolution of the texture of a silica aerogel during sintering is studied by thermoporometry. During the first stages of the densification the macroporous volume drops strongly while the mesoporous volume seems to be constant. This behavior is in contradiction with sintering models which predict that the sintering rate is faster for bodies with smaller particles or pores. In fact the analysis of the micropore size distribution shows that the sintering of the mesopores is responsible for macropore decrease.
Influence of the fluorine-oxygen substitution on the ionic conductivity properties of lithium tellurite glasses
Authors: REAU J. M. , TANGUY B. , PORTIER J. , ROJO J. M. , SANZ J. , HERRERO M. P.
Published: July 2007

A large range of glassy compositions has been found inside the ternary LiF-Li2O-TeO2 system. The influence of the fluorine-oxygen substitution on the ionic conduction properties of (50-x)LiO0.5-(x)LiF-(50)TeO2 ([MATH]) glasses has been investigated. These results have been correlated with the data relative to ion distribution and microstructure obtained by NMR and TEM. A maximum of conductivity associated with a minimum of activation energy is observed for [MATH]. The composition dependence of conductivity with rising x can be explained by a progressive decrease of the F-F associations around the Te4+ ions and a simultaneous increase of the Li-F associations. The clustering of the Li+ and F- ions produces small domains which hinder the Li+ ions diffusion in these glasses.
Reversible and irreversible electrical switching in TeO2-V2O5 based glasses
Authors: MAZURIER F. , LÉVY M. , SOUQUET J. L.
Published: July 2007

The switching phenomenon observed in electronically conductive glasses corresponds to a sudden decrease in electrical resistance of the sample when a large electric field is applied. A simple electrothermal model is developed which takes into account only a Joule effect overheating of the material. In a temperature range below the glass transition temperature, Tg, the switching is reversible. On the other hand, in a temperature range above Tg, a conductive crystalline phase is irreversibly formed leading to a permanent high conductivity state.
Non gaussian distributions in disordered systems studied by the cumulant expansion of EXAFS
Authors: DALBA G. , FORNASINI P. , ROCCA F. , SADOC A.
Published: July 2007

To test the effectiveness of the cumulant method for asymmetric distributions we measured and analyzed EXAFS in the anharmonic compound [MATH]-AgI from 23 to 410 K. The physical consistency of the so obtained cumulants has been evaluated from their temperature dependence and checked against the results from model distributions.
The Lamé equation in shell membrane theory
Authors: Schief W. K. , Szereszewski A. , Rogers C.
Published: July 2007

A classical nonlinear shell membrane system has recently been demonstrated to have underlying integrable structure. Here, a wide class of corresponding parallel membranes is shown to be generated via a Schrödinger equation of Lamé type. This class is characterized by the existence of a multiplicity of stress distributions for a given membrane geometry. A variety of viable membrane geometries such as generalized Dupin cyclides are constructed explicitly together with the associated one-parameter families of stress resultants. A Lax pair which encapsulates both the Gauss-Mainardi-Codazzi and constrained equilibrium equations is also recorded.
Electron spin resonance study on H6+, H5D+, H4D2+, and H2D4+ in solid parahydrogen
Authors: Kumagai Jun , Inagaki Hiroki , Kariya Susumu , Ushida Takahiro , Shimizu Yuta , Kumada Takayuki
Published: July 2007

We carried out an electron spin resonance (ESR) study on hydrogen ion radicals produced by radiolysis of solid para-H2. In addition to quartet ESR lines proposed to be H2+-core H6+ (D2d) ions in solid para-H2 [T. Kumada et al., Phys. Chem. Chem. Phys. 7, 776 (2005)], we newly observed totally more than 50 resolved lines in γ-ray irradiated solid para-H2–ortho-D2 (1mol%) and para-H2–HD (1mol%) mixtures. We assigned these lines to be isotope substituents of H2+-core H6+ ions such as H5D+, H4D2+, and H2D4+ throughout the comparison of their ESR parameters with theoretical results. These results provide a conclusive evidence that H2+-core H6+ ions are generated in irradiated solid hydrogens. Analysis of the EPR spectrum and ab initio calculations predicts D2d symmetry of the H6+ ions, whereas a lowering symmetry (D2d→C2v) induced by asymmetric nuclear wave function is observed in H5D+ and H4D2+. We also observed isotope-substitution reactions such as H6++D2→H4D2++H2 and H6++HD→H5D++H2, which are analogous to the well-known isotope-condensation reactions of H3+ in dark nebula, H3++HD→HD2++H2 and HD2++HD→D3++H2.
First-principles analysis of interfacial nanoscaled oxide layers of bonded N- and P-type GaAs wafers
Authors: Ouyang Hao , Chiou Hsiao-Hao , Wu YewChung Sermon , Cheng Ji-Hao , Ouyang Wen
Published: July 2007

First-principles analysis is applied in relating microstructures with properties of interfacial nanoscaled oxide layers of bonded N- and P-type GaAs wafers. Using high-resolution transmission electron microscope results, the detailed atomic arrangements of materials specimen can be obtained and fed into the first-principles calculations. Therefore, the corresponding electronic structure and associated property can be reliably derived to identify responsible microstructural features. The electrical performance is found to be closely related to the variation of nanosized interface morphology and types of wafers.
Kinetic lattice grand canonical Monte Carlo simulation for ion current calculations in a model ion channel system
Authors: Hwang Hyonseok , Schatz George C. , Ratner Mark A.
Published: July 2007

An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann mean field theory. Calculation of reaction field due to induced charges on the channel/water and membrane/water boundaries is carried out using a basis-set expansion method [Im and Roux, J. Chem. Phys. 115, 4850 (2001)]. Calculation of ion currents, electrostatic potentials, and ion concentrations, as obtained from the KLGCMC/MF simulations, shows good agreement with Poisson-Nernst-Planck (PNP) theory predictions when the channel and membrane have the same dielectric constant as water. If the channel and membrane have a lower dielectric constant than water, however, there is a considerable difference between the KLGCMC/MF and PNP predictions. This difference is attributed to the reaction field, which is missing in PNP theory. It is demonstrated that the reaction field as well as fixed charges in the channel play key roles in selective ion transport. Limitations and further development of the current KLGCMC/MF approach are also discussed.
Hydrogen bond dynamics and water structure in glucose-water solutions by depolarized Rayleigh scattering and low-frequency Raman spectroscopy
Authors: Paolantoni Marco , Sassi Paola , Morresi Assunta , Santini Sergio
Published: July 2007

The effect of glucose on the relaxation process of water at picosecond time scales has been investigated by depolarized Rayleigh scattering (DRS) experiments. The process is assigned to the fast hydrogen bonding dynamics of the water network. In DRS spectra this contribution can be safely separated from the slower relaxation process due to the sugar. The detected relaxation time is studied at different glucose concentrations and modeled considering bulk and hydrating water contributions. As a result, it is found that in diluted conditions the hydrogen bond lifetime of proximal water molecules becomes about three times slower than that of the bulk. The effect of the sugar on the hydrogen bond water structure is investigated by analyzing the low-frequency Raman (LFR) spectrum sensitive to intermolecular modes. The addition of glucose strongly reduces the intensity of the band at 170cm−1 assigned to a collective stretching mode of water molecules arranged in cooperative tetrahedral domains. These findings indicate that proximal water molecules partially lose the tetrahedral ordering typical of the bulk leading to the formation of high density environments around the sugar. Thus the glucose imposes a new local order among water molecules localized in its hydration shell in which the hydrogen bond breaking dynamics is sensitively retarded. This work provides new experimental evidences that support recent molecular dynamics simulation and thermodynamics results.
Improvement of dielectric properties of Ba0.6Sr0.4TiO3 thin films by MgO doping
Authors: Chiu Ming-Chieh , Yao Hsiao-Chiang , Huang Chueh-Jung , Shieu Fuh-Sheng
Published: July 2007

MgO-doped Ba0.6Sr0.4TiO3 (BST) thin films were synthesized by rf magnetron sputtering at substrate temperature of 750°C using single-phase targets with different MgO contents ranging from 0to5mol%. Microstructure, dielectric constant, and leakage current density of the MgO-doped BST films were characterized to understand the influence of the MgO dopant on film properties. Polycrystalline and perovskite phase solid solution films with a dense microstructure were obtained in all deposition conditions. The thickness of the 0,2,and5mol% MgO-doped BST films was measured to be 190, 140, and 150nm, respectively. The electrical and dielectric properties of the BST-containing capacitors are both found to be improved significantly by doping MgO in the BST films. The voltage-dependent capacitance C-V increases with increasing MgO doping up to 5mol%. The evidence for the asymmetric distribution of charge carriers in the MgO–BST film is derived from the interfacial layer. The leakage current density of the 5mol% MgO-doped BST capacitors is nearly two orders of magnitude lower and the dielectric constant is about 45% times higher than that of the undoped BST capacitors. Correlation of the material properties with dielectric properties suggests that the 5mol% MgO-doped BST films are the optimal choice for applications.
Measurement of propagation velocity of bound electromagnetic fields in near zone
Authors: Kholmetskii A. L. , Missevitch O. V. , Smirnov-Rueda R.
Published: July 2007

We start with the general approach based on conventional solutions to Maxwell’s equations and show that in the near zone of macroscopic electromagnetic sources the electromotive force produced in receiving loop antenna is intimately linked to the fundamental structure as well as to causal properties of the classical electromagnetic field as a superposition of bound and radiation components. As a consequence, we propose and implement a direct experimental procedure for the correct identification of retarded positions of bound field contributions on the oscilloscope time scale as a function of a distance from the emitting loop antenna. It provides unambiguous empirical information on causal characteristics of bound electromagnetic fields. According to the observation of no retardation inside the near zone of the emitting loop antenna, the experimental evidence for nonlocal properties of bound electromagnetic fields is reported.
Ab initio calculations on SnCl2 and Franck-Condon factor simulations of its ã-X̃ and B̃-X̃ absorption and single-vibronic-level emission spectra
Authors: Lee Edmond P. F. , Dyke John M. , Mok Daniel K. W. , Chow Wan-ki , Chau Foo-tim
Published: July 2007

Minimum-energy geometries, harmonic vibrational frequencies, and relative electronic energies of some low-lying singlet and triplet electronic states of stannous dichloride, SnCl2, have been computed employing the complete-active-space self-consistent-field/multireference configuration interaction (CASSCF/MRCI) and/or restricted-spin coupled-cluster single-double plus perturbative triple excitations [RCCSD(T)] methods. The small core relativistic effective core potential, ECP28MDF, was used for Sn in these calculations, together with valence basis sets of up to augmented correlation-consistent polarized-valence quintuple-zeta (aug-cc-pV5Z) quality. Effects of outer core electron correlation on computed geometrical parameters have been investigated, and contributions of off-diagonal spin-orbit interaction to relative electronic energies have been calculated. In addition, RCCSD(T) or CASSCF/MRCI potential energy functions of the X̃A11, ãB13, and B̃B11 states of SnCl2 have been computed and used to calculate anharmonic vibrational wave functions of these three electronic states. Franck-Condon factors between the X̃A11 state, and the ãB13 and B̃B11 states of SnCl2, which include anharmonicity and Duschinsky rotation, were then computed, and used to simulate the ã-X̃ and B̃-X̃ absorption and corresponding single-vibronic-level emission spectra of SnCl2 which are yet to be recorded. It is anticipated that these simulated spectra will assist spectroscopic identification of gaseous SnCl2 in the laboratory and/or will be valuable in in situ monitoring of SnCl2 in the chemical vapor deposition of SnO2 thin films in the semiconductor gas sensor industry by laser induced fluorescence and/or ultraviolet absorption spectroscopy, when a chloride-containing tin compound, such as tin dichloride or dimethyldichlorotin, is used as the tin precursor.
Quadrupole contribution to the third-order optical activity spectroscopy
Authors: Choi Jun-Ho , Cho Minhaeng
Published: July 2007

Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studying biomolecular and chemical reaction dynamics of chiral molecules. Only recently, the two-dimensional (2D) circularly polarized photon echo (CP-PE) spectroscopy of polypeptides and a photosynthetic light-harvesting complex were discussed, where the beam configuration was specifically controlled in such a way to eliminate the quadrupole contribution to the CP-PE signal. In this paper, we generalize the CP-PE spectroscopy by including the transition quadrupole contributions from peptide amide I vibrational transition and chlorophyll electronic transition. By using a density functional theory calculation method, the corresponding amide I vibrational and chlorophyll Qy electronic transition quadrupole tensor elements are determined. Amplitude of nonlinear optical transition pathway involving a quadrupole transition is found to be comparable to those of magnetic dipole terms for two different cases considered, i.e., dipeptides and photosynthetic antenna complex. However, due to the rotational averaging factors, the overall quadrupole contribution is an order of magnitude smaller than the magnetic dipole contribution. This suggests that the conventional 2D photon echo method and experimental scheme can be directly used to measure the 2D CP-PE signal from proteins and molecular complexes and that the 2D CP-PE signal is mainly dictated by the magnetic dipole contribution.
Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices
Authors: Peto Myron , Sen Taner Z. , Jernigan Robert L. , Kloczkowski Andrzej
Published: July 2007

We enumerated all compact conformations within simple geometries on the two-dimensional (2D) triangular and three-dimensional (3D) face centered cubic (fcc) lattice. These compact conformations correspond mathematically to Hamiltonian paths and Hamiltonian circuits and are frequently used as simple models of proteins. The shapes that were studied for the 2D triangular lattice included m×n parallelograms, regular equilateral triangles, and various hexagons. On the 3D fcc lattice we generated conformations for a limited class of skewed parallelepipeds. Symmetries of the shape were exploited to reduce the number of conformations. We compared surface to volume ratios against protein length for compact conformations on the 3D cubic lattice and for a selected set of real proteins. We also show preliminary work in extending the transfer matrix method, previously developed by us for the 2D square and the 3D cubic lattices, to the 2D triangular lattice. The transfer matrix method offers a superior way of generating all conformations within a given geometry on a lattice by completely avoiding attrition and reducing this highly complicated geometrical problem to a simple algebraic problem of matrix multiplication.