bluuebunny/crossref_metadata_2025 huggingface dataset:
Antiviral Activity of Benzimidazole Derivatives. I. Antiviral Activity of 1‐Substituted‐2‐[(Benzotriazol‐1/2‐yl)methyl]benzimidazoles
Authors: Tonelli Michele , Paglietti Giuseppe , Boido Vito , Sparatore Fabio , Marongiu Fabio , Marongiu Esther , La Colla Paolo , Loddo Roberta
Published: November 2008

Forty‐three 2‐[(benzotriazol‐1/2‐yl)methyl]benzimidazoles, bearing either linear (dialkylamino)alkyl‐ or bulkier (quinolizidin‐1‐yl)alkyl moieties at position 1, were evaluated in cell‐based assays for cytotoxicity and antiviral activity against viruses representative of two of the three genera of the Flaviviridae family, i.e. Flaviviruses (Yellow Fever Virus (YFV)) and Pestiviruses (Bovine Viral Diarrhoea Virus (BVDV)), as Hepaciviruses can hardly be used in routine cell‐based assays. Compounds were also tested against representatives of other virus families. Among ssRNA+ viruses were a retrovirus (Human Immunodeficiency Virus type 1 (HIV‐1)), two picornaviruses (Coxsackie Virus type B2 (CVB2), and Poliovirus type‐1, Sabin strain (Sb‐1)); among ssRNA− viruses were a Paramyxoviridae (Respiratory Syncytial Virus (RSV)) and a Rhabdoviridae (Vesicular Stomatitis Virus (VSV)) representative. Among double‐stranded RNA (dsRNA) viruses was a Reoviridae representative (Reo‐1). Two representatives of DNA virus families were also included: Herpes Simplex type 1, (HSV‐1; Herpesviridae) and Vaccinia Virus (VV; Poxviridae). Most compounds exhibited potent activity against RSV, with EC50 values as low as 20 nM. Moreover, some compounds, in particular when bearing a (quinolizidin‐1‐yl)alkyl residue, were also moderately active against BVDV, YFV, and CVB2.
New Phytotoxic Metabolites from Pestalotiopsis sp. HC02, a Fungus Residing in Chondracris rosee Gut
Authors: Zhang Ying Lao , Ge Hui Ming , Li Fang , Song Yong Chun , Tan Ren Xiang
Published: November 2008

Two new phytotoxic γ‐lactones, pestalotines A and B (1 and 2, resp.), along with 4‐oxo‐4H‐pyran‐3‐acetic acid (3) and 6‐hydroxyramulosin (=3,4,4a,5,6,7‐hexahydro‐6,8‐dihydroxy‐3‐methyl‐1H‐2‐benzopyran‐1‐one; 4), were isolateded from the culture of Pestalotiopsis sp. HC02, a fungus residing in the Chondracris rosee gut. Structures of the new metabolites were elucidated on the basis of their IR, NMR, and MS data. Pestalotines A and B (1 and 2, resp.) significantly inhibited the radical growth of Echinochloa crusgalli with IC50 values of 1.85×10−4 and 2.50×10−4 M, respectively, comparable to that of 2‐(2,4‐dichlorophenoxy)acetic acid (0.94×10−4 M) used as a positive control.
Synthesis, Characterization, and Antifungal Activity of Boron‐Containing Thiosemicarbazones
Authors: Hicks Justin W. , Kyle Christian B. , Vogels Christopher M. , Wheaton Susan L. , Baerlocher Felix J. , Decken Andreas , Westcott Stephen A.
Published: November 2008

Addition of thiosemicarbazide, 4‐allylthiosemicarbazide, and 4‐phenylthiosemicarbazide to (formylphenyl)boronic acids affords a series of thiosemicarbazones containing boronic acids. Addition of 2‐formylphenylboronic acid to the thiosemicarbazides gave the corresponding cyclic 2,3,1‐benzodiazaborines. All new compounds have been investigated for potential antifungal activity.
Study of Antimalarial Activity of Chemical Constituents from Diospyros quaesita
Authors: Ma Cui‐Ying , Musoke Sebisubi Fred , Tan Ghee Teng , Sydara Kongmany , Bouamanivong Somsanith , Southavong Bounhoong , Soejarto D. Doel , Fong Harry H. S. , Zhang Hong‐Jie
Published: November 2008

Bioassay‐directed fractionation led to the isolation of seven compounds from a sample of the dried leaves, twigs, and branches of Diospyros quaesita Thw. (Ebenaceae). One of the isolates, betulinic acid 3‐caffeate (1), showed in vitro antimalarial activity against Plasmodium falciparum clones D6 (chloroquine‐sensitive) and W2 (chloroquine‐resistant) with IC50 values of 1.40 and 0.98 μM, respectively. Evaluation of compound 1 in the human oral epidermoid (KB) cancer cell line revealed cytotoxicity at ED50 of 4.0 μM. In an attempt to reduce the cytotoxicity of 1, the acetylated derivative 1a and betulinic acid (1b) were prepared. Of the seven isolates, diospyrosin (2) was determined to be a new neolignan. In addition to 1, other known compounds isolated in this study were pinoresinol, lariciresinol, N‐benzoyl‐L‐phenylalaninol, scopoletin, and poriferast‐5‐en‐3β,7α‐diol. The structure of 2 was elucidated based on spectroscopic data analysis including 1D‐ and 2D‐NMR, and HR‐ESI‐MS.
Identification of the Chemotypes of Ocimum forskolei and Ocimum basilicum by NMR Spectroscopy
Authors: Fatope Majekodunmi O. , Marwah Ruchi G. , Al Hadhrami Nabil M. , Onifade Anthony K. , Williams John R.
Published: November 2008

The chemotypes of Ocimum forskolei Benth and Ocimum basilicum L. growing wild in Oman have been established by 13C‐NMR analyses of the vegetative and floral oils of the plants. The chemotypes, estragole for O. forskolei and linalool for O. basilicum, suggested by 13C‐NMR fingerprinting were also confirmed by GC‐FID and GC/MS analyses. The oil of O. forskolei demonstrated better activities against bacteria and dermatophytes. The significance of the presence of estragole and linalool in the volatile oils of plants whose fragrances are traditionally inhaled, added to food, or rubbed on the skin are discussed.
Investigation of Biosynthetic Pathways to Hydroxycoumarins During Post‐Harvest Physiological Deterioration in Cassava Roots by Using Stable Isotope Labelling
Authors: Bayoumi Soad A. L. , Rowan Michael G. , Beeching John R. , Blagbrough Ian S.
Published: November 2008

Cassava (Manihot esculenta Crantz) is an important starch‐rich crop, but the storage roots only have a short shelf‐life due to post‐harvest physiological deterioration (PPD), which includes the over‐production and polymerisation of hydroxycoumarins. Key aspects of coumarin secondary‐metabolite biosynthesis remain unresolved. Here we exploit the accumulation of hydroxycoumarins to test alternative pathways for their biosynthesis. Using isotopically labelled intermediates (p‐coumarate‐2‐13C, caffeate‐2‐13C, ferulate‐2‐13C, umbelliferone‐2‐18O and esculetin‐2‐18O), we show that the major biosynthetic pathway to scopoletin and its glucoside, scopolin, in cassava roots during PPD is through p‐coumaric, caffeic and then ferulic acids. An alternate pathway through 2′,4′‐dihydroxycinnamate and umbelliferone leads to esculetin and esculin. We have used C18O2‐carboxylate‐labelled cinnamic and ferulic acids, and feeding experiments under an atmosphere of 18O2, to investigate the o‐hydroxylation and cyclisation steps. We demonstrate that the major pathway is through o‐hydroxylation and not via a proposed spirolactone‐dienone intermediate.
Evidence for Dual Pathway in Through‐Space Singlet Energy Transfers in Flexible Cofacial Bisporphyrin Dyads
Authors: Pognon Grégory , Wytko Jennifer A. , Harvey Pierre D. , Weiss Jean
Published: November 2008

Flexible “pacman” scaffolds built upon a calix[4]arene platform bearing a [18]crown‐6 ether and either two OH functions or two OPr groups at the lower rim have been used to generate donor–acceptor (D–A) dyads incorporating a zinc–porphyrin donor and a free‐base porphyrin acceptor. Through‐space singlet energy transfer (SET) in the D–A dyads was studied by time‐resolved fluorescence spectroscopy. Although the effects of conformational changes are well documented when the chromophores switch from a non‐cofacial to a cofacial arrangement, little is known about flexible pacman scaffolds in which the changes are limited to the distance between the chromophores. The known SET rates for reported, geometrically well‐defined, rigid pacman D–A dyads were used as calibration to estimate the D–A distances in the flexible pacman dyads. Due to the flexibility of the calix[4]arene spacer, the D–A dyads adopt a “closed” or “open” geometry that is tuned by intramolecular hydrogen bonds (OH⋅⋅⋅[18]crown‐6 ether) and by solvent interactions. Changes in the SET rates between the open and closed geometries were surprisingly less dramatic than expected, and are explained by a dual SET pathway that is specific to the calix[4]arene platform. Time‐resolved fluorescence studies support the hypothesis that, for the “open” conformer, the preferred through space SET pathway (i.e., at the shortest distance) is located within the calix[4]arene cavity through the cofacial phenyl groups. For the “closed” conformer, the preferred through space SET route is located between the zinc and free‐base porphyrins.
Fluorescence Emission from 2,6‐Naphthylene‐Bridged Mesoporous Organosilicas with an Amorphous or Crystal‐Like Framework
Authors: Mizoshita Norihiro , Goto Yasutomo , Kapoor Mahendra P. , Shimada Toyoshi , Tani Takao , Inagaki Shinji
Published: November 2008

We report that 2,6‐naphthylene‐bridged periodic mesoporous organosilicas exhibit unique fluorescence behavior that reflects molecular‐scale periodicities in the framework. Periodic mesoporous organosilicas consisting of naphthalene–silica hybrid frameworks were synthesized by hydrolysis and condensation of a naphthalene‐derived organosilane precursor in the presence of a template surfactant. The morphologies and meso‐ and molecular‐scale periodicities of the organosilica materials strongly depend on the synthetic conditions. The naphthalene moieties embedded within the molecularly ordered framework exhibited a monomer‐band emission, whereas those embedded within the amorphous framework showed a broad emission attributed to an excimer band. These results suggest that the naphthalene moieties fixed within the crystal‐like framework are isolated in spite of their densely packed structure, different from conventional organosilica frameworks in which only excimer emission was observed for both the crystal‐like and amorphous frameworks at room temperature. This key finding suggests a potential to control interactions between organic groups and thus the optical properties of inorganic/organic hybrids.
Prathap's best‐fit paradigm and optimal strain recovery points in indeterminate tapered bar analysis using linear element
Authors: Mukherjee Somenath , Jafarali P.
Published: November 2008

In stress analysis procedures using the finite element method, where the results are generated through approximations using interpolation functions, there is a need to establish optimal points in a typical element that correspond to the exact values of stresses and strains. Conventionally, Gauss' points and Barlow's points are used as optimal points for stress recovery. In this paper it is shown that the justification for the existence of optimal strain/stress recovery points, referred to as Prathap points in an element, is a consequence of the best‐fit paradigm, originally proposed by Prathap through the stress correspondence principle.

Through the analysis of a statically indeterminate structure like a simple bar of linearly varying elastic rigidity with fixed ends, the existence of Prathap's points has been demonstrated through the best‐fit paradigm that remains valid even for statically indeterminate problems in a subtle manner. The present paper reconciles the prima facie, yet misleading, violation of the best‐fit rule with the fundamental theory of the finite element method, and effectively restores the validity of the best‐fit paradigm even for statically indeterminate problems in a deeper sense. Furthermore, consistent modified definitions of the global and local errors from the strain point of view are prescribed here. Copyright © 2008 John Wiley & Sons, Ltd.
Thermodynamic and Structural Characterization of the Transformation from a Metastable Low‐Density to a Very High‐Density Form of Supercooled TIP4P‐Ew Model Water
Authors: Paschek Dietmar , Rüppert Andreas , Geiger Alfons
Published: November 2008

We explore the phase diagram of the metastable TIP4P‐Ew liquid model water from 360 K down to 150 K at densities ranging from 0.950 to 1.355 g cm−3. In addition to the low‐density/high‐density (LDL/HDL) liquid–liquid transition, we observe a structural high‐density/very high‐density (HDL/VHDL) transformation for the lowest temperatures at 1.30 g cm−3. The characteristics of the isobars and isotherms suggest the presence of a stepwise HDL/VHDL transition with first‐order‐like appearance. In addition, we also identify an apparent pretransition at 1.24 g cm−3, which suggests that the experimentally detected LDA/VHDA transformation might evolve into a multiple‐step process with different local structures representing local minima in the free‐energy landscape. Such a scenario is supported by a pronounced correlation between the isothermal density dependence of the pressure, with a stepwise increase of the oxygen coordination number, due to the appearance of interstitial water molecules.
The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface
Authors: Paschek Dietmar , Pühse Matthias , Perez‐Goicochea Arnold , Gnanakaran S. , García Angel E. , Winter Roland , Geiger Alfons
Published: November 2008

We determine the shift and line shape of the amide I band of a model AK peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, which takes into account both the effect of hydrogen bonding and the intramolecular vibrational coupling. We consider a single isolated AK peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations, minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, which varies from pure water to the pure methanol solvent, a monotonous shift towards higher frequency of the IR amide I band of about 8 wavenumbers is observed. This shift towards higher frequency is comparable to the shift found in preliminary experimental data also presented here on the amide I′ band. The shift is found to be caused by two counter‐compensating effects. An intramolecular red shift of about 1.2 wavenumbers occurs, due to stronger intramolecular hydrogen bonding in a methanol‐rich environment. Dominating, however, is the intermolecular solvent‐dependent shift towards higher frequency of about 10 wavenumbers, which is attributed to the less effective hydrogen‐bond‐donor capabilities of methanol compared to water. The importance of the solvent contribution to the IR shift, as well as the significantly different hydrogen formation capabilities of water and methanol, makes the amide I band sensitive to composition changes in the local environment close to the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK peptide case, we observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent interface, supposedly promoted by the partially hydrophobic character of the AK peptide’s solvent‐accessible surface.
Protective effect of CPUX1, a progesterone, on hydrogen peroxide‐induced oxidative damage in PC12 cells
Authors: Ji Bian‐sheng , He Ling
Published: November 2008

The protective effect of CPUX1, a novel progesterone analog, on hydrogen peroxide (H2O2)‐induced oxidative damage was investigated in rat pheochromocytoma (PC12) cells. Following the exposure of PC12 cells to H2O2, there was a reduction in cell survival and activities of superoxide dismutase (SOD) and mitochondrial membrane potential (MMP) accompanied by increased levels of lactate dehydrogenase (LDH) release, malondialdehyde (MDA) production, and intracellular reactive oxygen species (ROS) and intracellular [Ca2+]i levels. Preincubation of cells with CPUX1 prior to H2O2 exposure attenuated all these changes mentioned and had a protective effect against H2O2‐induced toxicity in PC12 cells, indicating that the compound may have potential therapeutic benefit for CNS disorders influenced by oxidative damage. Drug Dev Res 69: 2008 ©2008 Wiley‐Liss, Inc.
Sensitivity and reproducibility of indirect calorimetry in measurement of resting metabolic rate
Authors: Karlsson Cecilia , Lystig Theodore , Hartford Marianne , Carlsson Björn
Published: November 2008

The aim of this study was to assess indirect calorimetry measurement of resting metabolic rate (RMR) with respect to sensitivity and reproducibility in a human study population suitable for early clinical studies to evaluate new anti‐obesity candidate drugs. Twenty‐four overweight, but otherwise healthy males were included in this randomized, single‐blind, placebo‐controlled, crossover study. Three different doses of epinephrine (0.005, 0.01, 0.03 µg · kg fat‐free mass (FFM)−1 · min−1) were used as active treatment. There were two identical study periods, separated by a 4‐week washout. Increases in RMR were seen with all tested concentrations of epinephrine when compared with placebo. Changes in RMR of ≥1.8% could be detected with 90% power in this crossover study design. The RMR values measured at the two study periods revealed a highly significant correlation (Spearman correlation 0.803, P=0.0007). To conclude, indirect calorimetry is a sensitive and robust means of measuring RMR. The method can be used to assess RMR in diverse clinical settings, even when considering modest differences. Drug Dev Res 69: 2008. © 2008 Wiley‐Liss, Inc.
Spatial gradients in ecohydrologic properties within a pinyon‐juniper ecosystem
Authors: Madsen M. D. , Chandler D. G. , Belnap J.
Published: November 2008

The influence of woody vegetation and biological soil crusts on infiltration capacity is one of the several uncertainties associated with the ecohydrologic effects of woody plant encroachment into arid and semi‐arid land systems. The objective of this study was to quantify the effects of Utah juniper (Juniperus osteosperma) and pinyon pine (Pinus edulis) on subcanopy and intercanopy ecohydrologic properties. We measured soil sorptivity, unsaturated hydraulic conductivity [K(h)], soil water content (SWC), and water repellency along radial line transects from under Juniperus and Pinus trees into the centre of the intercanopy space between trees. In the subcanopy, litter mounds, hydrophobic soils, and roots all appear to contribute to preferential flow to below‐surface soils via wetted patches. For both Juniperus and Pinus, K(h) was significantly lower in the subcanopy than the intercanopy average; however, line transect measurements did not show distinct boundaries in K(h) between the two regions. K(h) increased by eight‐fold across a gradient extending outward from near the edge of the canopy to approximately 2 times the canopy radius (CR). This suggests that the influence of these species on hydrologic properties extends significantly into the intercanopy region. Analysis of biological soil crust cover within the intercanopy showed that beyond the gradient zone, increasing structural development of biological soil crust was associated with increased K(h). Furthermore, these results indicate that the distance from the canopy and direction should be considered in the assessment and modelling of woody plant and biological soil crust influence on infiltration capacity. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitative proteomics by fluorescent labeling of cysteine residues using a set of two cyanine‐based or three rhodamine‐based dyes
Authors: Volke Daniela , Hoffmann Ralf
Published: November 2008

Despite all remarkable progress in gel‐based proteomics in recent years, there is still need to further improve quantification by decreasing the detection limits and increasing the dynamic range. These criteria are achieved best by fluorescent dyes that specifically stain the proteins either by adsorption after gel electrophoresis (in‐gel staining) or covalent coupling prior to gel electrophoresis (in‐solution staining). Here we report a multiplex analysis of protein samples using maleimide‐activated cyanine‐based (Cy3 and Cy5) and rhodamine‐based dyes (Dy505, Dy535, and Dy635) to permanently label all thiol‐groups of cysteine‐containing proteins. The detection limits in SDS‐PAGE were about 10 ng per band and even 2 ng for BSA due to its high content of cysteine residues. Thus only 5 μg protein of a mouse brain homogenate were analyzed by 2‐DE. Both cyanine‐ and rhodamine‐based dyes also stained proteins that did not contain cysteines, probably by reaction with amino groups. This side reactivity did not limit the method and might even extend its general use to proteins missing cysteine residues, but at a lower sensitivity. The dynamic range was more than two orders of magnitude in SDS‐PAGE and the Dy‐fluorophores did not alter the mobility of the tested proteins. Thus, a mixture of Dy505‐, Dy555‐, and Dy635‐labeled Escherichia coli lysates were separated by 2‐DE in a single gel and the three spot patterns relatively quantified.
Improved conditions for fluorescent staining of proteins with 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid in SDS‐PAGE
Authors: Cong Wei‐Tao , Hwang Sun‐Young , Jin Li‐Tai , Choi Jung‐Kap
Published: November 2008

A simple and sensitive fluorescent staining method for the detection of proteins in SDS‐PAGE, namely IB (improved 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid) stain, is described. Non‐covalent hydrophobic probe 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non‐specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.
Enantiomeric separation of glycidyl tosylate by CE: Application to the study of catalytic asymmetric epoxidation of allyl alcohol
Authors: Morante‐Zarcero Sonia , Crego Antonio L. , del Hierro Isabel , Sierra Isabel , Marina Maria Luisa
Published: November 2008

A CE method using CDs as chiral selectors was developed and validated to achieve the separation of glycidyl tosylate enantiomers originated by in situ derivatization of glycidol enantiomers obtained in asymmetric epoxidation of allyl alcohol with chiral titanium‐tartrate complexes as catalysts. The effects of the nature, pH and concentration of the buffer, the nature and concentration of chiral selector, the addition of SDS, methanol, ethanol or 2‐propanol, the capillary temperature, the effective capillary length and the applied voltage on the chiral resolution of glycidyl tosylate enantiomers were investigated. The best separation conditions were achieved using a Tris‐borate buffer mixture (50 and 25 mM, respectively) at pH=9.3 with a dual CD system consisting of 2.5% succinyl‐β‐CD and 1.0% β‐CD w/v at 15°C. A baseline separation (resolution∼2.0) of the glycidyl tosylate enantiomers was obtained in a relatively short time (less than 12 min). Satisfactory results were obtained in terms of linearity (r>0.99) and intermediate precision (RSD below 8.5%). The LOD and LOQ were 3.0 and 10.0 mg/L, respectively, and the recoveries ranged from 99.8 to 108.8%. Finally, the method was applied to the determination of the enantiomeric excess and the yield obtained in the asymmetric epoxidation of allyl alcohol employing chiral titanium‐tartrate complexes as catalysts after an in situ derivatization of glycidol enantiomers to glycidyl tosylate.
Pressure‐assisted CEC versus CEC using methacrylate‐based monolithic columns: Influence of the polymerization‐mixture composition
Authors: Tanret Indiana , Mangelings Debby , Vander Heyden Yvan
Published: November 2008

Pressure‐assisted CEC (pCEC) can either be performed on a CE instrument by adding pressure at the column inlet, or by applying voltage on a capillary liquid chromatography system. This study investigates the pressure's added value in pCEC using an LC instrument as well as the influence of the polymerization‐mixture composition on monolithic columns in such experimental circumstances. Two factors of the polymerization mixture, which is used to prepare the monolithic capillary columns, were varied according to an experimental design approach: the pore‐forming solvent/total monomer ratio and the pore‐forming solvents composition. Initially, the effect of the resulting stationary phase on the elution behavior of mainly pharmaceutical compounds was studied. Four responses were used to evaluate the effects on the chromatography: retention time, retention factor, peak asymmetry and number of theoretical plates. After processing the results, the stationary phase composition with the best chromatographic behavior was determined and tested. The advantageous properties of this stationary phase compared with the design center‐point column were demonstrated. Secondly, the results of these pCEC experiments were compared with those generated in an identical experimental setup previously performed using CEC. Chromatographic conditions were chosen so that the center‐point column showed similar retention in CEC and pCEC. The expected advantage (faster analysis) and drawback (decreased efficiency) of pCEC in the analysis of pharmaceuticals was evaluated. Analysis time and efficiency were both found to depend greatly on the porosity of the column. The conclusion of this comparison is that pCEC did not have a significant added value to CEC. However, this was mainly due to the instrument's limitation of the pressure‐driven flow over the column. A clear benefit of the pCEC setup was apparatus‐related, i.e. the presence of a loop injection system on the pCEC instrument, which avoids the injection problems that were occasionally observed in CEC.
Non‐hydrostatic 3D free surface layer‐structured finite volume model for short wave propagation
Authors: Cea L. , Stelling G. , Zijlema M.
Published: November 2008

In this paper a layer‐structured finite volume model for non‐hydrostatic 3D environmental free surface flow is presented and applied to several test cases, which involve the computation of gravity waves. The 3D unsteady momentum and mass conservation equations are solved in a collocated grid made of polyhedrons, which are built from a 2D horizontal unstructured mesh, by just adding several horizontal layers. The mesh built in such a way is unstructured in the horizontal plane, but structured in the vertical direction. This procedure simplifies the mesh generation and at the same time it produces a well‐oriented mesh for stratified flows, which are common in environmental problems. The model reduces to a 2D depth‐averaged shallow water model when one single layer is defined in the mesh. Pressure–velocity coupling is achieved by the Semi‐Implicit Method for Pressure‐Linked Equations algorithm, using Rhie–Chow interpolation to stabilize the pressure field. An attractive property of the model proposed is the ability to compute the propagation of short waves with a rather coarse vertical discretization. Several test cases are solved in order to show the capabilities and numerical stability of the model, including a rectangular free oscillating basin, a radially symmetric wave, short wave propagation over a 1D bar, solitary wave runup on a vertical wall, and short wave refraction over a 2D shoal. In all the cases the numerical results are compared either with analytical or with experimental data. Copyright © 2008 John Wiley & Sons, Ltd.
Pyridine‐4‐thiol and Amphoteric Analogs: Novel Protection of Aryl Bromides in Strong Alkali
Authors: Chen Wei‐Min , Cheng Chao , Li Bing‐Zhou , Ho Tse‐Lok , Cai Zhao‐Shuo , Wang Yuqiang , Sun Ping‐Hua
Published: November 2008

The use of pyridine‐4‐thiol (PT) to preserve certain aryl bromides in strong alkali is reported (Scheme 1). The presence of this additive or of some of its amphoteric analogs such as 3‐hydroxypyridin‐4(1H)‐ones suppresses the replacement of the Br‐substituent by hydroxide and alkoxide ions. A mechanistic interpretation of the effect is proposed.
Two New Endiandric Acid Analogs, a New Benzopyran, and a New Benzenoid from the Root of Beilschmiedia erythrophloia
Authors: Yang Ping‐Shin , Cheng Ming‐Jen , Chen Jih‐Jung , Chen Ih‐Sheng
Published: November 2008

Phytochemical investigation of the root of Beilschmiedia erythrophloia led to the isolation and structural elucidation of two new endiandric acid analogs, endiandric acids I and J (1 and 2, resp.), a new benzopyran, dehydrooligandrol methyl ether (3), and a new benzenoid, farnesylol (4), together with six known compounds. Their structures were established on the basis of extensive 1D‐ and 2D‐NMR analyses in combination with HR‐MS experiments.
Phenolic Derivatives from Fruits of Dipteryx lacuniferaDucke and Evaluation of Their Antiradical Activities
Authors: Júnior Gerardo Magela V. , de M. Sousa Cleyton Marcos , Cavalheiro Alberto J. , Lago João Henrique G. , Chaves Mariana H.
Published: November 2008

The fruits of Dipteryx lacunifera, known as ‘fava de morcego’ and ‘garampara’, comprise pleasant tasting kernels that contain high amounts of fatty acids (mainly oleic acid) and are commonly consumed by inhabitants of the northeast of Brazil. In the present study, the crude EtOH extract of the fruit kernels was separated into hexane‐, Et2O‐, AcOEt‐, and H2O‐soluble fractions. The Et2O fraction was found to exhibit the highest 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical‐scavenging activity in vitro, and was subjected to further fractionation. Column chromatography over silica gel and Sephadex LH‐20, followed by preparative HPLC‐C18, afforded (−)‐eriodictyol (1), (−)‐butin (2), luteolin (3), 3′,4′,7‐trihydroxyflavone (4), butein (5), and sulfuretin (6). The antiradical activities of compounds 1, 2, 4, and 6, together with the positive controls rutin, butylated hydroxy toluene (BHT), and tert‐butylhydroquinone (TBHQ), were evaluated with the DPPH assay and were found to decrease in the order rutin>4>1>6>2>TBHQ>BHT.
CXCL8/IL‐8 and CXCL12/SDF‐1α co‐operatively promote invasiveness and angiogenesis in pancreatic cancer
Authors: Matsuo Yoichi , Ochi Nobuo , Sawai Hirozumi , Yasuda Akira , Takahashi Hiroki , Funahashi Hitoshi , Takeyama Hiromitsu , Tong Zhimin , Guha Sushovan
Published: November 2008

CXC‐chemokines are involved in the chemotaxis of neutrophils, lymphocytes and monocytes. However, role of these chemokines in tumorigenesis, especially with regard to interaction between tumor and its microenvironment, has not been clearly elucidated. The purpose of this study was to analyze the co‐operative role of CXCL8 and CXCL12 in the tumor‐stromal interaction in pancreatic cancer (PaCa). Using enzyme‐linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT‐PCR), we initially confirmed the expression of ligands and receptors, respectively, of CXC‐chemokines in PaCa and stromal cells. We examined the co‐operative role of CXCL8 and CXCL12 in proliferation/invasion of PaCa and human umbilical vein endothelial cells (HUVECs), and in HUVEC tube‐formations through tumor‐stromal interaction by MTS, Matrigel invasion, and angiogenesis assays, respectively. We detected expression of CXCR4, but not CXCR2, in all PaCa cells and fibroblasts. PaCa cells secreted CXCL8, and fibroblast cells secreted CXCL12. CXCL8 production in PaCa was significantly enhanced by CXCL12, and CXCL12 production in fibroblasts was significantly enhanced by co‐culturing with PaCa. CXCL8 enhanced proliferation/invasion of HUVECs but did not promote proliferation/invasion of PaCa. Both recombinant and PaCa‐derived CXCL8 enhanced tube formation of HUVECs that were co‐cultured with fibroblast cells. CXCL12 enhanced the proliferation/invasion of HUVECs and the invasion of PaCa cells but had no effect on tube formation of HUVEC. We showed that PaCa‐derived CXCL8 and fibroblast‐derived CXCL12 cooperatively induced angiogenesis in vitro by promoting HUVEC proliferation, invasion, and tube formation. Thus, corresponding receptors CXCR2 and CXCR4 are potential antiangiogenic and antimetastatic therapeutic targets in PaCa. © 2008 Wiley‐Liss, Inc.
Myelodysplastic syndromes and acute myeloid leukemia in cats infected with feline leukemia virus clone33 containing a unique long terminal repeat
Authors: Hisasue Masaharu , Nagashima Naho , Nishigaki Kazuo , Fukuzawa Isao , Ura Shigeyoshi , Katae Hiromi , Tsuchiya Ryo , Yamada Takatsugu , Hasegawa Atsuhiko , Tsujimoto Hajime
Published: November 2008

Feline leukemia virus (FeLV) clone33 was obtained from a domestic cat with acute myeloid leukemia (AML). The long terminal repeat (LTR) of this virus, like the LTRs present in FeLV from other cats with AML, differs from the LTRs of other known FeLV in that it has 3 tandem direct 47‐bp repeats in the upstream region of the enhancer (URE). Here, we injected cats with FeLV clone33 and found 41% developed myelodysplastic syndromes (MDS) characterized by peripheral blood cytopenias and dysplastic changes in the bone marrow. Some of the cats with MDS eventually developed AML. The bone marrow of the majority of cats with FeLV clone33 induced MDS produced fewer erythroid and myeloid colonies upon being cultured with erythropoietin or granulocyte‐macrophage colony‐stimulating factor (GM‐SCF) than bone marrow from normal control cats. Furthermore, the bone marrow of some of the cats expressed high‐levels of the apoptosis‐related genes TNF‐α and survivin. Analysis of the proviral sequences obtained from 13 cats with naturally occurring MDS reveal they also bear the characteristic URE repeats seen in the LTR of FeLV clone33 and other proviruses from cats with AML. Deletions and mutations within the enhancer elements are frequently observed in naturally occurring MDS as well as AML. These results suggest that FeLV variants that bear URE repeats in their LTR strongly associate with the induction of both MDS and AML in cats. © 2008 Wiley‐Liss, Inc.
Putative functional polymorphisms of MMP9 predict survival of NSCLC in a Chinese population
Authors: Jin Guangfu , Miao Ruifen , Hu Zhibin , Xu Lin , Huang Xinen , Chen Yijiang , Tian Tian , Wei Qingyi , Boffetta Paolo , Shen Hongbing
Published: November 2008

Matrix metalloproteinases (MMPs) play a crucial role in cancer progression and their over‐expression is often associated with unfavorable survival of non‐small cell lung cancer (NSCLC). Because genetic variants can alter expression level or biological activity of MMPs, we hypothesized that potentially functional single nucleotide polymorphisms (SNPs) in key MMP genes may be associated with the survival of NSCLC patients. We selected and genotyped 14 putative functional SNPs in six MMP genes (MMP1, MMP2, MMP3, MMP7, MMP9 and MMP12) using PCR‐RFLP methods in 561 NSCLC patients. Kaplan‐Meier method with the log‐rank test and Cox proportional hazard models were used for the survival analyses. The C‐1562T, Arg279Gln and Arg668Gln polymorphisms in MMP9 were significantly associated with survival of patients with NSCLC (log‐rank p values = 0.032, 0.038 and 0.036, respectively). The C‐1562T and Arg668Gln loci were in complete linkage disequilibrium (r2 = 1). Patients carrying the 668Gln allele had improved survival with a median survival time (MST) of 51.6 months, compared with 21.8 months for those with the 668Arg/Arg genotype (log‐rank p = 0.010). In contrast, the 279Gln/Gln genotype was associated with a significantly shortened MST (17.3 months, log‐rank p = 0.030) in the recessive model. In the final multivariate Cox regression model, 279Gln/Gln was identified as an independent prognostic factor with an adjusted hazard ratio of 1.60 (95% confidence interval 1.07–2.41). The MMP9 Arg279Gln and Arg668Gln SNPs are potential predictors of survival in NSCLC patients. © 2008 Wiley‐Liss, Inc.
Evidence for the accelerations of sea level on multi‐decade and century timescales
Authors: Woodworth P. L. , White N. J. , Jevrejeva S. , Holgate S. J. , Church J. A. , Gehrels W. R.
Published: November 2008

A modification in the rate of change of sea level (i.e. an ‘acceleration’ or ‘nonlinear trend’) is an important climate‐related signal, which requires confirmation and explanation. In this study, the evidence for accelerations in regional and global average sea level on timescales of several decades and longer is reviewed by inter‐comparison of the recent findings of different researchers and by inspection of original tide gauge records. Most sea‐level data originate from Europe and North America, and both the sets display evidence for a positive acceleration, or ‘inflexion’, around 1920–1930 and a negative one around 1960. These inflexions are the main contributors to reported accelerations since the late 19th century, and to decelerations during the mid‐ to late 20th century. However, these characteristic features are not always found in records from other parts of the world. Although some aspects of the sea‐level time series are consistent with changes in rates of globally averaged temperature changes, volcanic eruptions and natural climate variability, modelling undertaken so far has been unable to describe these features adequately. This emphasizes the need for a major enhancement of the sea‐level data set, especially for those parts of the world without long tide gauge records, in order to obtain greater insight into the spatial dependence of accelerations. A number of complementary methods must be employed, of which salt marsh techniques offer the possibility of obtaining time series similar to those that would have been obtained from coastal tide gauges. Copyright © 2008 Royal Meteorological Society
Interannual relations between South American rainfall and tropical sea surface temperature anomalies before and after 1976
Authors: Kayano Mary Toshie , de Oliveira Cristiano Prestrelo , Andreoli Rita Valéria
Published: November 2008

The differences between 1948–1976 and 1977–2002 periods in the interannual relationships of South American precipitation with sea surface temperature (SST) indices in selected oceanic sectors are documented using correlation analyses. For the total correlation between the eastern equatorial Pacific (EEP) and tropical South Atlantic (TSA) indices and the precipitation, the differences between the two periods reflect, in part, the El Niño‐Southern Oscillation (ENSO) teleconnections over South America, with the Pacific decadal oscillation (PDO) background acting to enhance (weaken) the correlations when ENSO and PDO are in the same (opposite) phase. For the total correlation between the tropical North Atlantic (TNA) and southwest South Atlantic (SWA) indices and precipitation, the results here suggest that the differences between the two periods might be reflected as variations in the Bolivian high‐pressure system. Both the TNA and TSA indices may act to weaken the positive ENSO relations with precipitation over central and eastern Brazil during the cold PDO phase. These analyses provide indications that the ENSO relationship with the TSA shows differences between the two analysed periods. Copyright © 2008 Royal Meteorological Society
CE determination of quinolones in the presence of bovine serum albumin
Authors: Qin Weidong , Liu Qingchun , Fan Yongxia
Published: November 2008

This article describes the influence of bovine serum albumin (BSA) as an additive on the capillary electrophoresis–potential gradient determination of five quinolones, enoxacin, norfloxacin, ofloxacin, fleroxacin, and pazufloxacin. With 10 mg/L of BSA present in the buffer of 30 mM Tris and 3 mM phosphoric acid at pH 9, the detection limits of the five quinolones were in the range of 0.24–0.68 mg/L, i. e. 5.8–16.5‐fold lower than those obtained with the buffer devoid of BSA, and the analysis time was shortened. We suggest that the inner wall‐adsorbed BSA suppresses the adsorption of quinolones and simultaneously enhances the electroosmotic flow rate. Our experiments indicated that adopting the potential gradient detection technique could eliminate the interference of the UV‐active proteins on the detection of quinolones that would occur with conventional optical detection, and therefore offer high detection sensitivity. As a demonstration, the method was applied to the determination of QNs in fortified chicken muscle sample with satisfactory results.
Optimizing capillary column backflush to improve cycle time and reduce column contamination
Authors: Klee Matthew S.
Published: November 2008

Interest in decreasing cycle times in capillary GC analyses has driven much of the instrumental developments of the last decade. Recent developments in GC instrumentation now make it reasonable to consider backflushing capillary columns on a routine basis. Significant reduction in analysis and total cycle times (typically 15–50% depending on the application) are readily achieved for analyses that currently require an extended temperature program and bakeout period to remove retained sample components and column contaminants. Setup and optimization of backflush conditions are relatively straight forward as long as some basic concepts are well understood. The parameters affecting capillary column backflushing are described. Examples are shown that help visualize what happens during backflush. The relationship between oven ramp rate and flow turns out to be an important variable that dictates minimum backflush times in temperature programmed CGC. Backflush times corresponding to 2–5 void volumes in the reversed direction are usually sufficient for backflushing, if performed after each temperature programmed run.
Sol–gel polydimethylsiloxane/poly(vinylalcohol)‐coated stir bar sorptive extraction of organophosphorus pesticides in honey and their determination by large volume injection GC
Authors: Yu Chunhe , Hu Bin
Published: November 2008

A PDMS/poly(vinylalcohol) (PDMS/PVA) film prepared through a sol–gel process was coated on stir bars for sorptive extraction, followed by liquid desorption and large volume injection–GC–flame photometric detector (LVI–GC–FPD) for the determination of five organophosphorus pesticides (OPPs) (phorate, fenitrothion, malathion, parathion, and quinalphos) in honey. The preparation reproducibility of PDMS/PVA‐coated stir bar ranged from 4.3 to 13.4% (n = 4) in one batch, and from 6.0 to 12.6% (n = 4) in batch to batch. And one prepared stir bar can be used for more than 50 times without apparent coating loss. The significant parameters affecting stir bar sorptive extraction (SBSE) were investigated and optimized. The LODs for five OPPs ranged from 0.013 (parathion) to 0.081 μg/L (phorate) with the RSDs ranging from 5.3 to 14.2% (c = 1 μg/L, n = 6). The proposed method was successfully applied to the analysis of five OPPs in honey.
Association between adenomatosis polyposis coli functional status and microsomal prostaglandin E synthase‐1 expression in colorectal cancer
Authors: Elander Nils , Zhou Jianlin , Ungerbäck Jonas , Dimberg Jan , Söderkvist Peter
Published: November 2008

Bioactive metabolites downstream of cyclooxygenase‐2 (COX‐2) generated prostaglandin H2 (PGH2), in particular prostaglandin E2 (PGE2), are thought to play critical roles during the development of colorectal tumors. Previous reports reveal that defects of the tumor suppressor adenomatosis polyposis coli (APC) contribute to COX‐2 upregulation in colon tumor cells. We investigated whether a similar relation was present between APC functional status and the expression of microsomal prostaglandin E synthase‐1 (mPGES‐1), which acts downstream of COX‐2 and catalyses the terminal conversion of PGH2 into PGE2. Surprisingly, mPGES‐1 mRNA and protein levels were upregulated upon induction of a wild type‐APC carrying vector in HT29 colon cancer cells, and downregulated following siRNA silencing of APC in HCT‐116 cells. mPGES‐1 was overall enhanced in human colorectal tumor specimens versus corresponding non‐tumor mucosa and, in accordance with data on HT29 and HCT116 cells, higher levels of mPGES‐1 were observed among tumors carrying wild type versus mutant APC. RNAi silencing of β‐catenin and luciferase assays regarding the mPGES‐1 promoter region did not reveal a role for APC or β‐catenin/Tcf in controlling mPGES‐1 gene transcription. However, RNA degradation assays in HT29 cells revealed a suppressed degradation of mPGES‐1 in the presence of wild type APC, implying that mPGES‐1 mRNA is stabilized in the APC wild type state. Collectively, we demonstrate a novel association between APC functional status and mPGES‐1 expression in colorectal tumor cells, being most likely related to reduced mPGES‐1 mRNA degradation rate in the APC wild type state. © 2008 Wiley‐Liss, Inc.
Convergence of coercive approximations for a model of gradient type in poroplasticity
Authors: Owczarek Sebastian
Published: November 2008

We study the existence theory to the quasi‐static initial‐boundary‐value problem of poroplasticity. In this article the classical quasi‐static Biot model is considered for soil consolidation coupled with a nonlinear system of differential equations. This work, for the poroplasticity model of monotone‐gradient type, presents a convergence result of the coercive approximation to the solution of the original noncoercive problem. Copyright © 2008 John Wiley & Sons, Ltd.
Glucosinolates inBrassicavegetables: The influence of the food supply chain on intake, bioavailability and human health
Authors: Verkerk Ruud , Schreiner Monika , Krumbein Angelika , Ciska Ewa , Holst Birgit , Rowland Ian , De Schrijver Remi , Hansen Magnor , Gerhäuser Clarissa , Mithen Richard , Dekker Matthijs
Published: November 2008

Glucosinolates (GLSs) are found inBrassicavegetables. Examples of these sources include cabbage, Brussels sprouts, broccoli, cauliflower and various root vegetables (e.g. radish and turnip). A number of epidemiological studies have identified an inverse association between consumption of these vegetables and the risk of colon and rectal cancer. Animal studies have shown changes in enzyme activities and DNA damage resulting from consumption ofBrassicavegetables or isothiocyanates, the breakdown products (BDP) of GLSs in the body. Mechanistic studies have begun to identify the ways in which the compounds may exert their protective action but the relevance of these studies to protective effects in the human alimentary tract is as yet unproven.In vitrostudies with a number of specific isothiocyanates have suggested mechanisms that might be the basis of their chemoprotective effects. The concentration and composition of the GLSs in different plants, but also within a plant (e.g. in the seeds, roots or leaves), can vary greatly and also changes during plant development. Furthermore, the effects of various factors in the supply chain ofBrassicavegetables including breeding, cultivation, storage and processing on intake and bioavailability of GLSs are extensively discussed in this paper.
Retracted:Comments on ‘Upper bound solution to elasticity problems: A unique property of the linearly conforming point interpolation method (LC‐PIM)’ by G. R. Liu and G. Y. Zhang, International Journal for Numerical Methods in Engineering, 2008
Authors: Moitinho de Almeida J. P.
Published: November 2008

The following article from International Journal for Numerical Methods in Engineering, Comments on ‘Upper bound solution to elasticity problems: A unique property of the linearly conforming point interpolation method (LC‐PIM)’ by G. R. Liu and G. Y. Zhang, published online on 19 June 2008 in Wiley InterScience (www.interscience.wiley.com), has been retracted by agreement between the authors, the journal Editor‐in‐Chief, Ted Belytschko and John Wiley & Sons, Ltd. The retraction has been agreed due to the article being published out of sequence with a related article and with insufficient citation details.