bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential Proton‐Release Channels in Bacteriorhodopsin
Authors: Chaumont Alain , Baer Marcel , Mathias Gerald , Marx Dominik
Published: November 2008

The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton‐transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen‐bonded networks, which may include internal water molecules. The terminal step of the proton‐transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton‐release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen‐bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.
Effects of Isomerization on the Measured Thermochemical Properties of Deprotonated Glycine/Protic‐Solvent Clusters
Authors: Nieckarz Robert J. , Atkins Chad G. , McMahon Terry B.
Published: November 2008

The thermochemical properties associated with the formation of an isomeric distribution of ROH⋅⋅⋅NH2CH2COO− clusters (R=H, CH3, C2H5) are measured by using high‐pressure mass spectrometry. A comparison of the measured properties with calculated values provides new insights into the thermochemical effects arising from the isomeric nature of this clustering system. When the distribution of isomers is correctly accounted for, the measured values of ΔH°, ΔS°, and ΔG°298 consistently agree, to a very high degree of accuracy, with those predicted by MP2(full)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) calculations.
Dendrimers with a Pentaphenylene Core: A Photophysical Study
Authors: Bergamini Giacomo , Ceroni Paola , Balzani Vincenzo , Kandre Ramchandra , Lukin Oleg
Published: November 2008

Novel dendrimers G2PC and G4PC consisting of a p‐pentaphenylene core (PC) appended in the para position with two second‐generation (G2) or two fourth‐generation (G4) sulfonimide branches and two n‐octyl chains, as well as a model compound of the pentaphenylene core (G0PC), are prepared. The photophysical properties (absorption, emission, and excitation spectra; fluorescence decay lifetime; and fluorescence anisotropy spectra) of the three compounds are investigated under different experimental conditions (dichloromethane solution and solid state at 293 K, dichloromethane/methanol rigid matrix at 77 K). In the absorption spectra contributions from both the branches and the core can be clearly identified. The fluorescence spectra show only the characteristic fluorescence of the pentaphenylene unit with λmax around 410 nm in fluid solution and 420 nm in the solid state. In solution the fluorescence quantum yields are 0.78, 0.76, and 0.72 for G0PC, G2PC, and G4PC, respectively, and the fluorescence lifetime is about 0.7 ns in all cases. Energy transfer from the chromophoric groups of the dendrimer branches to the core does not occur. The three compounds show the same, high steady‐state anisotropy value (0.35) in dilute rigid‐matrix solution at 77 K. In dichloromethane at 293 K, the increasing anisotropy values along the series G0PC (0.17), G2PC (0.27), and G4PC (0.32), with increasing molecular volume of the three compounds, show that depolarization takes place by molecular rotation. In the solid state the anisotropy is very low (0.015, 0.017, and 0.035 for G0PC, G2PC, and G4PC, respectively), probably because of fast depolarization via energy migration.
L‐type Ca2+ channel opener BayK 8644‐induced Ca2+ influx and Ca2+ release in human oral cancer cells (OC2)
Authors: Chi Chao‐Chuan , Huang Chorng‐Chih , Chien Jau‐Min , Chu Sau‐Tung , Chen Wei‐Chuan , Chang Hong‐Tai , Lin Ko‐Long , Tsai Jeng‐Yu , Liao Wei‐Chuan , Chou Chiang‐Ting , Jan Chung‐Ren
Published: November 2008

The effect of BayK 8644, a chemical widely used to activate L‐type Ca2+ channels, on cytosolic free Ca2+ concentrations ([Ca2+]i) in human oral cancer cells (OC2) has not been explored to date. The present study examined whether BayK 8644 altered basal [Ca2+]i levels in suspended OC2 cells by using fura‐2. BayK 8644 (10 pM–10 µM) increased [Ca2+]i in a concentration‐dependent manner. The Ca2+ signal was reduced partly by removing extracellular Ca2+. BayK 8644‐induced Ca2+ influx was blocked by nifedipine, but was not altered by the store‐operated Ca2+ entry inhibitors, econazole and SKF96365; protein kinase C modulators phorbol 12‐myristate 13‐acetate (PMA) and GF109203X; the protein kinase A inhibitor H89; and the phospholipase A2 inhibitor, aristolochic acid. In Ca2+‐free medium, after pretreatment with 1 µM BayK 8644, 1 µM thapsigargin (an endoplasmic reticulum Ca2+ pump inhibitor)‐induced [Ca2+]i rises were abolished; and conversely, thapsigargin pretreatment abolished BayK 8644‐induced [Ca2+]i rises. Inhibition of phospholipase C with U73122 did not change BayK 8644‐induced [Ca2+]i rises. Collectively, in OC2 cells, BayK 8644 induced [Ca2+]i rises by causing phospholipase C‐independent Ca2+ release from the endoplasmic reticulum; and Ca2+ influx via L‐type Ca2+ channels. Drug Dev Res 69: 2008. © 2008 Wiley‐Liss, Inc.
The woody weed encroachment puzzle: gathering pieces
Authors: Patrick Graz F.
Published: November 2008

Increases in woody plant densities in savanna grazing lands worldwide have resulted in a decline in the grazing capacity of these rangelands. At present, the actual cause of the problem is unknown although a vast body of literature deals with various aspects relevant to the issue.

It is generally assumed, however, that the changes in the tree:grass ratio are a response to changes in soil‐water development brought about by rangeland utilization. These utilization patterns differ from those under which the savanna system evolved. While changes in physiognomy are very prominent, these are generally preceded by changes in grass species assemblage.

The development of species composition has been used as an indicator of rangeland condition for many years; the increase or decrease of individual species is considered in this context. Thus far, however, the shift from perennial to annual grasses has not been evaluated for its effect on soil moisture development, and subsequent implications for woody plant establishment and growth.

The review presented here consolidates the existing information in order to provide a basis for understanding the woody weed encroachment problem. Copyright © 2008 John Wiley & Sons, Ltd.
CEC with tris(2,2′‐bipyridyl) ruthenium(II) electrochemiluminescent detection
Authors: Li Haijuan , Liu Xiaoqing , Niu Wenxin , Zhu Shuyun , Fan Lishuang , Shi Lihong , Xu Guobao
Published: November 2008

For the first time, CEC was coupled with tris(2,2‐bipyridyl) ruthenium(II) (
Ru(bpy) electrochemiluminescence detection. Efficient CEC separations of proline, putrescine, spermidine and spermine were achieved when the pH of the mobile phase is in the range of 3.5–7.0. The optimum mobile phase for CEC separation is much less acidic than that for CZE separation, which matches better with the optimum pH for Ru(bpy) electrochemiluminescence detection and dramatically shortens the analysis time because of larger EOF at higher pH. The time for CEC separation of the polyamines is less than 12.5 min, which is about half as much as the time needed for CZE. The detection limits were 1.7, 0.2, and 0.2 μM for putrescine, spermidine, and spermine, respectively. The RSD of retention time and peak height of these polyamines were less than 0.85 and 6.1%, respectively. The column showed good long‐term stability, and the RSD of retention time is below 5% for 150 runs over one‐month use. The method was successfully used for the determination of polyamines in urine samples.
Focusing and stabilization of bis‐intercalating dye–DNA complexes for high‐sensitive CE‐LIF DNA analysis
Authors: Wang Zhixin , Wang Chao , Yin Junfa , Li Tao , Song Maoyong , Lu Meiling , Wang Hailin
Published: November 2008

Multiple labeling of nucleic acids by intercalative dyes is a promising method for ultrasensitive nucleic acid assays. The properties of the fast dissociation and instability of dye–DNA complexes may prevent from their wide applications in CE‐LIF nucleic acid analysis. Here, we describe an optimum CE focusing method by using appropriately paired sample and separation buffers, Tris‐glycine buffer and Tris‐glycine‐acetic acid buffer. The developed method was applied in both uncoated and polyacrylamide coated fused‐silica capillary‐based CE‐LIF analysis while the sample and separation buffers were conversely used. The complexes of intercalative dye benzoxazolium‐4‐pyridinium dimer and dsDNA were greatly focused (separation efficiency: 1.8 million theoretical plates per meter) by transient isotachophoresis mechanism in uncoated capillary, and moderately focused by transient isotachophoresis in combination of field amplified sample stacking and further stabilized by the paired buffer in polyacrylamide coated capillary. Based on the developed focusing strategy, an ultrasensitive DNA assay was developed for quantitation of calf thymus dsDNA (from 0.02 to 2.14 pM). By the use of an excitation laser power as low as 1 mW, the detection limits of calf thymus dsDNA (3.5 kb) are 7.9 fM in concentration and 2.4×10−22 mol (150 molecules) in mass. We further demonstrate that the non‐gel sieving CE‐LIF analysis of DNA fragments can be enhanced by the same strategy. Since the presented strategy can be applied to uncoated and coated capillaries and does not require special device, it is also reasonable to extend to the applications in chip‐based CE DNA analysis.
A new approximation for spectral velocity ordinates at short periods
Authors: Gupta Vinay K.
Published: November 2008

Response spectrum methods in earthquake‐resistant design sometimes require information on the spectral velocity (SV) for a given single‐degree‐of‐freedom oscillator and specified seismic hazard. SV has been conventionally approximated as pseudo spectral velocity (PSV) in the case of lightly damped structures that are not too flexible. This study shows that the PSV approximation may lead to large overestimation errors when the structure is stiffer to the ground motion and the ground motion is a long‐period motion. It is also shown that a new approximation requiring the use of peak ground acceleration of the motion may significantly reduce these errors. Copyright © 2008 John Wiley & Sons, Ltd.
Deformation during exhumation of medium‐ and high‐grade metamorphic rocks in the Variscan chain in northern Sardinia (Italy)
Authors: Carosi Rodolfo , Frassi Chiara , Montomoli Chiara
Published: November 2008

The Anglona and SW Gallura regions represent key places to investigate the tectonic evolution of medium‐ and high‐grade metamorphic rocks cropping out in northern Sardinia (Italy). From south to north we distinguish two different metamorphic complexes recording similar deformation histories but different metamorphic evolution: the Medium Grade Metamorphic Complex (MGMC) and the High Grade Metamorphic Complex (HGMC).

After the initial collisional stage (D1 deformation phase), both complexes were affected by three contractional deformational phases (D2, D3 and D4) followed by later extensional tectonics. The D2 deformation phase was the most significant event producing an important deformation partitioning that produced localized shearing and folding domains at the boundary between the two metamorphic complexes.

We highlight the presence of two previously undocumented systems of shear belts with different kinematics but analogous orientation in the axial zone of Sardinia. They became active at the boundary between the MGMC and HGMC from the beginning of D2. They formed a transpressive regime responsible for the exhumation of the medium‐ and high‐grade metamorphic rocks, and overall represent a change from orthogonal to orogen‐parallel tectonic transport. Copyright © 2008 John Wiley & Sons, Ltd.
Synthetic Studies on Camptothecins. Part 1
Authors: Zhang Li‐Peng , Bao Yong , Kuang Yun‐Yan , Chen Fen‐Er
Published: November 2008

A six‐step asymmetric total synthesis of (20S)‐camptothecin (1) has been accomplished in 25% overall yield starting from the known pyridone 3. The key steps in this synthesis are the chemoselective Ni‐catalyzed hydrogenation of 3‐cyanopyridone 6 to 3‐formylpyridone 7 in AcOH/pyridine/H2O and the Davis asymmetric hydroxylation of tricyclic lactone 4 utilizing a chiral N‐sulfonyloxaziridine into (4′S)‐tricyclic hydroxylactone 2.
Two Novel Triterpenoids from Portulaca oleracea L.
Authors: Xin Hai‐Liang , Xu Yan‐Feng , Hou Yin‐Huan , Zhang Ya‐Ni , Yue Xiao‐Qiang , Lu Jin‐Cai , Ling Chang‐Quan
Published: November 2008

Two novel triterpenoids, (2α,3α)‐3‐{[4‐O‐(β‐D‐glucopyranosyl)‐β‐D‐xylopyranosyl]oxy}‐2,23‐dihydroxy‐30‐methoxy‐30‐oxoolean‐12‐en‐28‐oic acid (1) and (2α,3α)‐2,23,30‐trihydroxy‐3‐[(β‐D‐xylopyranosyl)oxy]olean‐12‐en‐28‐oic acid (2) were isolated from Portulaca oleracea L., and they both showed weak cytotoxic activity assayed with the MTT method.
Eight New Diterpenoids from the Roots of Euphorbia nematocypha
Authors: He Fei , Pu Jian‐Xin , Huang Sheng‐Xiong , Xiao Wei‐Lie , Yang Li‐Bin , Li Xiao‐Nian , Zhao Yong , Ding Jian , Xu Cheng‐Hui , Sun Han‐Dong
Published: November 2008

From the dried roots of Euphorbia nematocypha, eight new diterpenoids, with ent‐atisane (i.e., 1–5) and isopimarane (i.e., 6–8) type skeletons, together with five known compounds, were isolated. The structures of these new compounds were elucidated by spectroscopic data. Compounds 1–8 were evaluated for their cytotoxicity against a small panel of human cancer cell lines.
Three New Alkaloids, Paxiphyllines C – E, from Daphniphyllum paxianum
Authors: Zhang Yu , Di Ying‐Tong , Liu Hai‐Yang , Li Chun‐Shun , Tan Cheng‐Jian , Zhang Qiang , Fang Xin , Li Shun‐Lin , Hao Xiao‐Jiang
Published: November 2008

Nine Daphniphyllum alkaloids, including three new ones, paxiphyllines C–E (1–3, resp.), were isolated from the twigs and the leaves of Daphniphyllum paxianum. Paxiphylline C (1) represents the first example of Daphniphyllum alkaloids with a carbonyldioxy group. Their structures were elucidated on the basis of spectroscopic data.
Adipokine genes and prostate cancer risk
Authors: Moore Steven C. , Leitzmann Michael F. , Albanes Demetrius , Weinstein Stephanie J. , Snyder Kirk , Virtamo Jarmo , Ahn Jiyoung , Mayne Susan T. , Yu Herbert , Peters Ulrike , Gunter Marc J.
Published: November 2008

Adiposity and adipocyte‐derived cytokines have been implicated in prostate carcinogenesis. However, the relationship of adipokine gene variants with prostate cancer risk has not been thoroughly investigated. We therefore examined common variants of the IL6, LEP, LEPR, TNF and ADIPOQ genes in relation to prostate cancer in a case‐control study nested within a large cohort of Finnish men. The study sample consisted of 1,053 cases of prostate cancer, diagnosed over an average 11 years of follow up, and 1,053 controls matched to the cases on age, intervention group and date of baseline blood draw. Logistic regression was used to model the relative odds of prostate cancer. We also examined genotypes in relation to serum insulin, IGF‐1 and IGF‐1:IGFBP‐3 among 196 controls. Variant alleles at three loci (−14858A>G, −13973A>C, −13736C>A) in a potential regulatory region of the LEP gene conferred a statistically significant 20% reduced risk of prostate cancer. For example, at the −14858A>G locus, heterozygotes and homozygotes for the A allele had an odds ratio (OR) of prostate cancer of 0.76 [95% confidence interval (CI) 0.62, 0.93] and 0.79 (95% CI 0.60, 1.04), respectively. At 13288G>A, relative to the GG genotype, the AA genotype was associated with a suggestive increased risk of prostate cancer (OR = 1.29; 95% CI 0.99,1.67; ptrend = 0.05). Polymorphisms in the IL6, LEPR, TNF and ADIPOQ genes were not associated with prostate cancer. Allelic variants in the LEP gene are related to prostate cancer risk, supporting a role for leptin in prostate carcinogenesis. © 2008 Wiley‐Liss, Inc.
Pathological activation of KIT in metastatic tumors of acral and mucosal melanomas
Authors: Ashida Atsuko , Takata Minoru , Murata Hiroshi , Kido Kenji , Saida Toshiaki
Published: November 2008

Recent studies showed KIT gene aberrations in a substantial number of melanomas on acral skin and mucosa, suggesting the therapeutic benefit of tyrosine kinase inhibitors, such as imatinib. We therefore examined the expression and mutations of KIT in 4 primary and 24 metastatic acral and mucosal melanomas. Immunohistochemistry revealed moderate or strong KIT protein expression in 13 (48%) tumors. Sequence analysis revealed K642E and D820Y mutations in two metastases. Amplification of KIT was identified by real‐time PCR in 4 tumors, including one that had K642E. Western blot analysis showed phosphorylation of the KIT receptor in 8 (62%) of 13 cryopreserved samples, indicating the frequent pathological activation of the receptor in vivo. Phosphorylation of KIT protein was detected in 2 tumors harboring KIT mutations, as well as in one tumor with KIT gene amplification. Furthermore, 5 tumors without detectable KIT gene aberrations showed phosphorylation of the KIT receptor. Expression of stem cell factor (SCF) in melanoma cells as well as stromal cells suggests SCF/KIT autocrine and paracrine activation in these tumors. Finally, we found significant growth suppressive effects of sunitinib in two acral melanoma cell lines; one harboring the D820Y mutation and one showing SCF‐dependent KIT activation. These results show pathological activation of KIT in a substantial number of metastatic tumors of acral and mucosal melanomas, and suggest a potential therapeutic benefit of sunitinib for these melanomas. © 2008 Wiley‐Liss, Inc.
Cytoplasmic accumulation of activated leukocyte cell adhesion molecule is a predictor of disease progression and reduced survival in oral cancer patients
Authors: Sawhney Meenakshi , Matta Ajay , Macha Muzafar A. , Kaur Jatinder , DattaGupta Siddhartha , Shukla Nootan K. , Ralhan Ranju
Published: November 2008

Activated leukocyte cell adhesion molecule (ALCAM) has been proposed to function as a cell surface sensor for cell density, controlling the transition between local cell proliferation and tissue invasion in cancer progression. Herein, we determined ALCAM expression in 107 oral squamous cell carcinomas (OSCCs), 78 oral lesions (58 hyperplasias and 20 dysplasias) and 30 histologically normal oral tissues using immunohistochemistry and correlated with clinicopathological parameters. Significant increase in ALCAM immunopositivity was observed from normal oral mucosa, hyperplasia, dysplasia to OSCCs (ptrend < 0.001). Increased ALCAM expression was observed in cytoplasm of epithelial cells as early as in hyperplasia (p = 0.001, OR = 3.8). Sixty‐five of 107 (61%) OSCCs showed significant overexpression of ALCAM protein in cytoplasm/membrane of tumor cells (p = 0.043; OR = 3.3) in comparison with the normal oral tissues. Among OSCCs, cytoplasmic ALCAM was associated with advanced tumor size, tumor stage and tobacco consumption. Importantly, cytoplasmic ALCAM was an independent predictor of poor prognosis of OSCCs in multivariate analysis (p = 0.012, OR = 6.2). In an attempt to understand the molecular basis of cytoplasmic localization of ALCAM, 14‐3‐3ζ and 14‐3‐3σ were identified as its novel binding partners in oral cancer cells. In conclusion, increased expression of ALCAM is an early event in oral tumorigenesis; its cytoplasmic accumulation in tumor cells is a predictor of poor prognosis of OSCCs, underscoring its potential as a candidate prognostic marker for oral cancer. © 2008 Wiley‐Liss, Inc.
Approximation of Nash equilibria in Bayesian games
Authors: Armantier Olivier , Florens Jean‐Pierre , Richard Jean‐Francois
Published: November 2008

We define a new concept of constrained strategic equilibrium (CSE) for Bayesian games. We show that a sequence of CSEs approximates an equilibrium under standard conditions. We also provide an algorithm to implement the CSE approximation method numerically in a broad class of Bayesian games, including games without analytically tractable solutions. Finally, we illustrate the flexibility of the CSE approximation with a series of auction examples, including a complex multi‐unit auction. Copyright © 2008 John Wiley & Sons, Ltd.
Variability in wintertime position and strength of the North Pacific jet stream as represented by re‐analysis data
Authors: Barton Neil P. , Ellis Andrew W.
Published: November 2008

The popular National Center for Environmental Prediction (NCEP)/National Center for Atmospheric Research (NCAR) re‐analysis database was used to create a mean winter seasonal jet stream database for the northern Pacific Ocean region for the period 1948–1949 through 2004–2005. Grids of mean seasonal 300 hPa scalar wind were used to determine the latitudinal position of the primary mid‐latitude jet on a longitudinal resolution of 2.5° from eastern Asia to western North America. The position and strength of the jet stream across this region are key determinants of winter precipitation variability downstream across the predominantly arid western region of North America.

Results show that the latitudinal position of the jet exhibits greater variance over the eastern half of the northern Pacific Ocean, while the greatest variance in the speed of the seasonal jet occurs across the central northern Pacific Ocean. A statistically significant increase in the speed of the mean seasonal jet occurred over the central area of the northern Pacific Ocean during the last half of the 20th century. A spatially consistent but statistically insignificant trend toward a more southerly position of the jet occurred during the study period. The results do not confirm current theories of a general pole‐ward shift in mid‐latitude jet streams in association with recent and future climate change, suggesting that such an observed or theoretical hemispheric shift may not necessarily be evident within a particular region or that any shift over the last 50 years has been less than the 2.5° resolution of the NCEP/NCAR dataset. The jet stream data support the connection between the jet and the Pacific‐North American atmospheric teleconnection pattern and between the jet and the oscillation of sea surface temperature anomalies in the northern Pacific Ocean known as the Pacific Decadal Oscillation. Copyright © 2008 Royal Meteorological Society
How do we tell which estimates of past climate change are correct?
Authors: Sherwood Steven C. , Titchner Holly A. , Thorne Peter W. , McCarthy Mark P.
Published: November 2008

Estimates of past climate change often involve teasing small signals from imperfect instrumental or proxy records. Success is often evaluated on the basis of the spatial or temporal consistency of the resulting reconstruction, or on the apparent prediction error on small space and time scales. However, inherent methodological trade‐offs illustrated here can cause climate signal accuracy to be unrelated, or even inversely related, to such performance measures. This is a form of the classic conflict in statistics between minimum variance and unbiased estimators. Comprehensive statistical simulations based on climate model output are probably the best way to reliably assess whether methods of reconstructing climate from sparse records, such as radiosondes or paleoclimate proxies, actually work on longer time scales. Copyright © 2008 Royal Meteorological Society
Nanomechanics of single silkworm and spider fibres: a Raman and micro‐mechanical in situ study of the conformation change with stress
Authors: Colomban Philippe , Dinh Hung Manh , Riand Jacques , Prinsloo Linda C. , Mauchamp Bernard
Published: November 2008

The combination of micro‐Raman spectroscopy and an advanced universal fibre tester (UFT) made it possible to probe at the nanoscale (through monitoring the modification of chemical bonds) the change in conformation (α‐helix, β‐sheet, etc.), macromolecular fibroin chain orientation and coupling during the application of stress, quantitatively. Different single fibres of silkworms (Bombyx mori, Gonometa rufobrunea, Gonometa postica) and a spider (Nephila madagascariensis) were tested in a dry environment and compared with the behaviour of keratin fibre. As observed previously for single keratin fibres, a direct relationship is observed between nano‐ and micro‐mechanical tensile behaviour. The phase transition plateau, well defined for some pristine B. mori fibres, disappears in degummed fibres, which indicates a structural modification and increasing disorder with chemical treatments. Stress‐controlled micro‐Raman analysis shows that a few modes involving CH2 and/or amide groups of β‐conformation chains undergo a wavenumber softening during the elastic behaviour (∼0–3%), although most of the modes are not affected. A different behaviour is observed for modes associated with ‘ordered’ and ‘disordered’ β‐sheets and helical chains. Larger softening is observed for lattice modes with increasing stress/strain, as expected. Structural changes and relationships with mechanical behaviour are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
NIR‐FT Raman, FT‐IR and surface‐enhanced Raman scattering spectra, with theoretical simulations on chloramphenicol
Authors: Sajan D. , Sockalingum G. D. , Manfait M. , Hubert Joe I. , Jayakumar V. S.
Published: November 2008

Chloramphenicol (CLM), originally derived from the bacterium Streptomyces venezuelae, is an inhibitor of bacterial ribosomal peptidyl transferase activity. The near infrared Fourier transform (NIR‐FT) Raman, surface‐enhanced Raman spectroscopy (SERS) and Fourier transform infrared (FT‐IR) spectral analyses of CLM, a potential antibacterial drug for the treatment of typhoid fever, were carried out along with density functional computations. The vibrational spectral analysis reveals that the CH2 asymmetric and symmetric stretching modes are shifted to higher wavenumbers than the computed values, owing to the electronic effects resulting from induction of methylene group with the adjacent electronegative atom. The lowering of CO stretching wavenumber is due to the presence of the strong electronegative atom, nitrogen, attached to the carbonyl carbon, causing large degree of molecular π‐electron delocalization and redistribution of electrons, which weakens the CO bond. The absence of a CH stretching vibration and the observed CH out‐of‐plane bending modes suggest that the CLM molecule may be adsorbed in a flat orientation with respect to the silver surface. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of polybrominated diphenyl ethers in sewage sludge by matrix solid‐phase dispersion and isotope dilution GC–MS
Authors: Sánchez‐Brunete Consuelo , Miguel Ester , Tadeo José L.
Published: November 2008

A method for the determination of 14 polybrominated diphenyl ethers (PBDEs) in sludge from wastewater treatment plants is presented. PBDEs were extracted by matrix solid‐phase dispersion assisted by sonication and determined by isotope dilution gas chromatography with electron impact mass spectrometric detection in the selected ion monitoring mode, using labelled 13C‐PBDEs as internal standards. The limits of detection and quantification for the tri‐ to hepta‐BDEs were in the range of 0.05 to 0.5 ng/g dry weight and 0.15 to 1.8 ng/g dry weight, respectively, and 1.6 ng/g dry weight and 5.6 ng/g dry weight for deca‐BDE‐209. The proposed analytical method was applied to determine PBDE levels in sewage sludge samples collected from 19 water treatment plants located in the province of Madrid (Spain). In all of the examined samples, BDE‐100 and BDE‐154 were the main compounds found with a mean concentration of 3.9 and 2.0 ng/g, respectively. PBDEs were detected in all of the samples, and their total concentrations not considering BDE‐209 were between 3.9 and 23.0 ng/g dry weight. The dominant PBDE congener in sewage sludge was BDE‐209, which constituted 38.7 to 97.3% of the total, and showed concentration levels ranging from 8.1 to 717.2 ng/g dry weight.
Impact of land use and land cover change on environmental degradation in lake Qinghai watershed, northeast Qinghai‐Tibet Plateau
Authors: Li X.‐Y. , Ma Y.‐J. , Xu H.‐Y. , Wang J.‐H. , Zhang D.‐S.
Published: November 2008

Lake Qinghai, the largest saline lake in China, covers 4234 km2 (2007) with a catchment area of 29 660 km2 on the northeastern margin of the Qinghai‐Tibet Plateau. The ecosystem of the lake is extremely vulnerable and sensitive to global climate change and human interference. However, little information is available on land use/cover change (LUCC) in Lake Qinghai watershed. Using a geographical information system (GIS) and remote sensing (RS), this study analysed land use and land cover change pattern in Lake Qinghai watershed between 1977 and 2004 and discussed major environmental issues in this area. LUCC analysis indicated that grassland (63 per cent) and water body (18 per cent) dominated in the watershed and the magnitude of the land use and land cover change was generally low; the percentage of the change of various land types relative to the total area was less than 1 per cent. From 1977 to 2004, cropland, sandy land, bare rock, salinized land, swampland and built‐up areas increased by 0·43, 0·35, 0·24, 0·06, 0·03 and 0·03 per cent of the total area, respectively; in contrast, water body, grassland and woodland decreased by 0·99, 0·22 and 0·05 per cent, respectively. Moreover, the area of LUCC tended to expand from places around the lake to the upper reaches of the watershed during the last three decades. The LUCC transition pattern was: woodland converted to grassland, grassland converted to cropland and water body converted to sandy land. Lake level decline and grassland degradation are major ecological and environmental problems in Lake Qinghai watershed. The level and area of the lake decreased at the rate of 6·7 cm a−1 and 6·4 km2 a−1, respectively, between 1959 and 2007, resulting in sandy land expansion and water quality deterioration. Lake level decline and area shrinkage was mainly attributed to climate change, but grassland degradation was mainly resulted from anthropogenic activities (increasing population, overgrazing and policy). Copyright © 2008 John Wiley & Sons, Ltd.
On the existence of finite energy weak solutions to the Navier–Stokes equations in irregular domains
Authors: Kukučka Peter
Published: November 2008

This paper studies the existence of weak solutions of the Navier–Stokes system defined on a certain class of domains in ℝ3 that may contain cusps. The concept of such a domain and weak energy solution for the system is defined and its existence is proved. However, thinness of cusps must be related to the adiabatic constant appearing in the pressure law. Copyright © 2008 John Wiley & Sons, Ltd.
Chardonnay grape seed procyanidin extract supplementation prevents high‐fat diet‐induced obesity in hamsters by improving adipokine imbalance and oxidative stress markers
Authors: Décordé Kelly , Teissèdre Pierre‐Louis , Sutra Thibault , Ventura Emilie , Cristol Jean‐Paul , Rouanet Jean‐Max
Published: November 2008

Studies reported the effects of polyphenols but not for grape polyphenols towards obesity. We analysed the effects of a polyphenolic grape seed extract (GSE) on obesity and oxidative stress in hamsters receiving a high‐fat diet (HFD). Three groups of hamsters received a standard diet (STD), or a HFD plus a daily gavage with water (Control, HFD) or a solution of GSE (HFD + GSE) for 12 wk. Plasma glucose, triglycerides (TG), insulin, leptin and adiponectin were measured. Oxidative stress was assessed by cardiac production of superoxide anion and NAD(P)H oxidase expression. After 12 wk, HFD increased abdominal fat as compared with standards. GSE avoided this feature. HFD led to higher plasma glucose, TG, insulin and greater insulin resistance (HOMA‐IR) values. GSE prevented in part these effects, reducing insulinemia and leptinemia by 16.5 and 45%, respectively, whereas adiponectin level increased by 61% compared with obese controls. GSE lowered glycemia and HOMA‐IR and strongly prevented cardiac production of superoxide by 74% and NAD(P)H oxidase expression by 30%. This is the first time that chronic consumption of grape phenolics is shown to reduce obesity development and related metabolic pathways including adipokine secretion and oxidative stress.
Computing the conditioning of the components of a linear least‐squares solution
Authors: Baboulin Marc , Dongarra Jack , Gratton Serge , Langou Julien
Published: November 2008

In this paper, we address the accuracy of the results for the overdetermined full rank linear least‐squares problem. We recall theoretical results obtained in (SIAM J. Matrix Anal. Appl. 2007; 29(2):413–433) on conditioning of the least‐squares solution and the components of the solution when the matrix perturbations are measured in Frobenius or spectral norms. Then we define computable estimates for these condition numbers and we interpret them in terms of statistical quantities when the regression matrix and the right‐hand side are perturbed. In particular, we show that in the classical linear statistical model, the ratio of the variance of one component of the solution by the variance of the right‐hand side is exactly the condition number of this solution component when only perturbations on the right‐hand side are considered. We explain how to compute the variance–covariance matrix and the least‐squares conditioning using the libraries LAPACK (LAPACK Users' Guide (3rd edn). SIAM: Philadelphia, 1999) and ScaLAPACK (ScaLAPACK Users' Guide. SIAM: Philadelphia, 1997) and we give the corresponding computational cost. Finally we present a small historical numerical example that was used by Laplace (Théorie Analytique des Probabilités. Mme Ve Courcier, 1820; 497–530) for computing the mass of Jupiter and a physical application if the area of space geodesy. Copyright © 2008 John Wiley & Sons, Ltd.
A theoretical and experimental study of the polar Diels–Alder cycloaddition of cyclopentadiene with nitrobenzodifuroxan
Authors: Steglenko Dmitry V. , Kletsky Mikhail E. , Kurbatov Sergey V. , Tatarov Artem V. , Minkin Vladimir I. , Goumont Régis , Terrier François
Published: November 2008

The mechanism of the Diels–Alder interaction of 4‐nitrobenzodifuroxan (NBDF) with cyclopentadiene (Cp), resulting in the highly stereoselective formation of the stable endo [2+4] adduct has been elucidated by combining density functional theory (DFT) and experimental studies. Calculations at the B3LYP/6‐31G* level reveal that this adduct does not derive from a direct normal electron demand cycloaddition process. Instead, the evidence is that the interaction proceeds initially through a very polar inverse electron demand process to afford the intermediate [4+2] cycloadduct. Then, this species undergoes a complete conversion into the more stable isomeric endo [2+4] adduct via a [3+3] Claisen‐type sigmatropic shift. The lifetime of the [4+2] intermediate was sufficient to allow its full1H NMR characterization at −10 °C. Viewing the results in the general context of the Diels–Alder reactivity of nitrobenzofuroxans, a noteworthy feature is that the similar behavior of NBDF and 4‐aza‐6‐nitrobenzofuroxan (ANBF) goes along with a similar positioning of the two compounds on the general electrophilicity scale of Parret al. Copyright © 2008 John Wiley & Sons, Ltd.
Theoretical study of neighboring group participation of methyl ω‐chloroesters elimination kinetics in the gas phase
Authors: Romero Mery Lorena , Cordova Tania , Chuchani Gabriel
Published: November 2008

The mechanisms of the homogeneous, unimolecular, gas‐phase elimination kinetics of several methyl ω‐chloroesters were examined by using the ‘ab initio’ and DFT level of theories. Theoretical calculations of dehydrochlorination of methyl 3‐chloropropionate suggest a planar concerted, non‐synchronous, four‐membered cyclic transition state to give methyl acrylate. However, the parallel competitive gas‐phase elimination of methyl 4‐chlorobutyrate and methyl 5‐chlrovalerate occurs through neighboring group participation to render methyl chloride and the corresponding lactone through a concerted, semi‐polar five‐ and six‐membered cyclic transition state type of mechanism. Calculated thermodynamic and kinetic parameters reasonably agree with the experimental values at DFT B3LYP/6‐31G* theory level. Geometrical parameters, NBO charges and bond indexes showed strong polarization at Cδ+···Clδ− bond in the transition state suggesting the breaking of CCl bond as rate‐determining factor for both dehydochlorination and lactone formation reactions. The synchronicity parameters suggest a concerted polar mechanism implying a TS which has ion‐pair character for lactone product formation. Copyright © 2008 John Wiley & Sons, Ltd.
Experimental and theoretical FT‐IR and FT‐Raman spectroscopic analysis of N1‐methyl‐2‐chloroaniline
Authors: Karabacak Mehmet , Kurt Mustafa , Ataç Ahmet
Published: November 2008

In this work, the experimental and theoretical vibrational spectra of N1‐methyl‐2‐chloroaniline (C7H8NCl) were studied. FT‐IR and FT‐Raman spectra of the title molecule in the liquid phase were recorded in the region 4000–400 cm−1 and 3500–50 cm−1, respectively. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method (B3LYP) with the 6‐311++G(d,p) basis set. The vibrational frequencies were calculated and scaled values were compared with experimental FT‐IR and FT‐Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. 13C and 1H NMR chemical shifts results were compared with the experimental values. The optimized geometric parameters (bond lengths and bond angles) were given and are in agreement with the corresponding experimental values of aniline and p‐methyl aniline. Copyright © 2008 John Wiley & Sons, Ltd.
Genome‐wide linkage scan for prostate cancer susceptibility from the university of michigan prostate cancer genetics project: Suggestive evidence for linkage at 16q23
Authors: Lange Ethan M. , Beebe‐Dimmer Jennifer L. , Ray Anna M. , Zuhlke Kimberly A. , Ellis Jaclyn , Wang Yunfei , Walters Sarah , Cooney Kathleen A.
Published: November 2008

BACKGROUND

Prostate cancer linkage studies have been used to localize rare and presumably highly penetrant cancer susceptibility genes. Underlying genetic heterogeneity, as well as the high sporadic background of the disease, has resulted in many signals that are often not reproducible between research studies.

METHODS

We conducted a SNP‐based genome wide linkage scan on 131 Caucasian prostate cancer families participating in the University of Michigan Prostate Cancer Genetics Project (PCGP).

RESULTS

The strongest evidence for linkage was detected at 16q23 (LOD = 2.70 at rs1079635). Prostate cancer linkage to the same region of 16q23 has been observed by others and the region contains several strong candidate genes including the known prostate cancer tumor suppressor genes ATBF1 and WWOX. This linkage signal was not detected in our prior linkage study on 175 PCGP families, illustrating the genetic heterogeneity underlying prostate cancer susceptibility.

CONCLUSIONS

Further linkage studies in combination with tumor analyses from linked families are in progress to identify the putative hereditary prostate cancer gene at 16q23. Prostate 69:385–391, 2009. © 2008 Wiley‐Liss, Inc.
Improving the interaction of Myc‐interfering peptides with Myc using molecular dynamics simulations
Authors: Jouaux Eva M. , Timm Barbara B. , Arndt Katja M. , Exner Thomas E.
Published: November 2008

Previously, a Myc‐interfering peptide (Mip) was identified for the targeted inactivation of the Myc:Max complex by the combination of rational design and an in vivo protein‐fragment complementation assay. In the subsequent work presented here, molecular dynamics simulations and free energy calculations based on the molecular mechanics GBSA method were performed to define the contribution of the different amino acids in the Myc:Mip coiled coil domain, and compared to wild‐type Myc:Max. For further optimization of the Myc interference, point mutations were introduced into Mip and analyzed, from which two showed much higher binding affinities in the computational studies in good agreement with the experiment. These mutants with very high potential for inactivation of Myc can now be used as starting point for further optimizations based on the computational as well as experimental protocols presented here. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Phonon sidebands in semiconductor luminescence
Authors: Feldtmann T. , Kira M. , Koch S. W.
Published: November 2008

A microscopic theory of LO‐phonon assisted photoluminescence in semiconductors is presented. In order to systematically describe Coulomb and light–matter interaction, a cluster‐expansion scheme is employed. The carrier–phonon coupling is treated non‐perturbatively within the polaron picture. Luminescence equations are derived, which produces phonon sidebands to arbitrary oder. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improving mixing length‐scale for stable boundary layers
Authors: Grisogono B. , Belušić D.
Published: November 2008

We intend to improve the ‘z‐less’ mixing length‐scale for parametrization of turbulence in the stable atmospheric boundary layers (SABL). Since the SABL structures are far from being fully understood today, their parametrizations or explicit treatment are still usually very sketchy in most mesoscale and climate models. Typically an over‐diffusion through the SABL occurs in most numerical models. With the ‘z‐less’ mixing length‐scale proposed here the over‐diffusion is absent. In particular, the mesoscale model used gave results similar to those from an improved (calibrated) Prandtl model, i.e. katabatic flow occupying the lower and more active part of the SABL developed in both models. The corresponding low‐level jet that is embedded in the strong near‐surface inversion appears similar in both models. Certain details vary, simply because of the very different nature of the models deployed. The results, that should be also valid for other types of SABL flows, could be used in different types of numerical modelling, parametrizations of the SABL, further development of analytical models and data interpretation. Copyright © 2008 Royal Meteorological Society
Robust output feedback learning control for induction motor servo drives
Authors: Tomei P. , Verrelli C. M. , Montanari M. , Tilli A.
Published: November 2008

This paper addresses the output feedback tracking control problem for induction motor servo drives with mechanical uncertainties: rotor angle, rotor speed and stator currents are assumed to be available for feedback. A robust adaptive learning control is designed under the assumption that the reference profile for the rotor angle is periodic with known period: it ‘learns’ the periodic disturbance signal by identifying the Fourier coefficients of any truncated approximation; ℒ︁2 and ℒ︁∞ transient performances are guaranteed in the ‘learning phase’. It is shown that, for any motor initial condition belonging to an arbitrary given compact set, by properly setting the control parameters: (i) the rotor position and flux modulus tracking errors exponentially converge to residual sets, which may be arbitrarily reduced by increasing the number of terms in the truncated Fourier series; (ii) when the unknown periodic disturbance can be represented by a finite Fourier series, the rotor position and flux modulus tracking errors exponentially converge to zero. As in field oriented‐control, the control algorithm generates references for the magnetizing flux component and for the torque component of the stator current leading to significant simplifications for current‐fed motors. Copyright © 2008 John Wiley & Sons, Ltd.
Semiparametric modeling of repeated measurements under outcome‐dependent follow‐up
Authors: Bůžková Petra , Lumley Thomas
Published: November 2008

In regression analysis of repeated measurements that are taken at subject‐specific times, the availability of the outcome data may be related to the past outcome and to other measured variables that are not in the intended regression model. In this paper we propose a natural extension of the semiparametric regression procedure of Lin and Ying (J. Am. Stat. Assoc. 2001; 96:103–126) by building a class of ‘inverse‐intensity‐rate‐ratio’ weighted estimators that accommodate such outcome‐dependent follow‐up. The estimators have a closed form, are √n‐consistent, asymptotically normal, and do not require estimation of any infinite‐dimensional parameters. We give several simulations to demonstrate the estimator's performance and show a sensitivity study under follow‐up with various degrees of dependence on outcome‐related variables. We illustrate our approach using data from a randomized health services research study with noncompliance to scheduled visits. Copyright © 2008 John Wiley & Sons, Ltd.
Funds of knowledge and discourses and hybrid space
Authors: Barton Angela Calabrese , Tan Edna
Published: November 2008

The findings reported on in this manuscript emerged from a design experiment conducted at a low‐income urban middle school intended to support the teacher in incorporating pedagogical practices supportive of students' everyday knowledge and practices during a 6th grade unit on food and nutrition from the LiFE curriculum. In studying the impact of the design experiment we noticed qualitative shifts in classroom Discourse marked by a changing role and understandings of the funds of knowledge students brought to science learning. Using qualitative data and grounded theory we present an analysis of the different types of funds of knowledge and Discourse that students brought into science class. We focus on how the students' strategic use of these funds augmented the learning experience of the students and the learning community as well as the learning outcomes. We discuss the implications these funds of knowledge and Discourses had on the development of three related third space transformations: physical, political, and pedagogical. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 46: 50–73, 2009