bluuebunny/crossref_metadata_2025 huggingface dataset:
Managing irrigation demand to improve seasonality of river flows
Authors: Khan Shahbaz , Ahmad Aftab , Malano Hector M.
Published: July 2008

Human interventions often lead to unsustainable river systems. There is always a trade‐off between level of socio‐economic gains from consumptive use in the river system and the need to maintain the natural seasonality of river flows supporting the ecosystem function. In the case of the Murrumbidgee River, Australia, irrigation demand is concentrated in the summer season while natural inflows to the river occur during the winter season. The summer‐dominated irrigation water demand has created environmental and supply problems by altering the natural flow regime. This paper presents a hydrologic assessment of a range of irrigation demand management options for improving the natural seasonality of the river flow. Among the possible alternatives, change of cropping pattern by achieving a better mix of summer and winter crops is recommended as the most feasible alternative, which can also save up to 211 million m3 of water yearly. This water can then be released during the winter time to augment the environmental flows of the river. Other irrigation demand management options explored in this paper include aquifer storage and recovery, on‐farm and off‐farm water savings and construction of intermediate surface water storages. Copyright © 2008 John Wiley & Sons, Ltd.
Molecular dynamics/order parameter extrapolation for bionanosystem simulations
Authors: Miao Yinglong , Ortoleva Peter J.
Published: July 2008

A multiscale approach, molecular dynamics/order parameter extrapolation (MD/OPX), to the all‐atom simulation of large bionanosystems is presented. The approach starts with the introduction of a set of order parameters (OPs) automatically generated with orthogonal polynomials to characterize the nanoscale features of bionanosystems. The OPs are shown to evolve slowly via Newton's equations, and the all‐atom multiscale analysis (AMA) developed earlier (Miao and Ortoleva, J Chem Phys 2006, 125, 44901) demonstrates the existence of their stochastic dynamics, which serve as the justification for our MD/OPX approach. In MD/OPX, a short MD run estimates the rate of change of the OPs, which is then used to extrapolate the state of the system over time that is much longer than the 10−14 second timescale of fast atomic vibrations and collisions. The approach is implemented in NAMD and demonstrated on cowpea chlorotic mottle virus (CCMV) capsid structural transitions (STs). It greatly accelerates the MD code and its underlying all‐atom description of the nanosystems enables the use of a universal interatomic force field, avoiding recalibration with each new application as needed for coarse‐grained models. The source code of MD/OPX is distributed free of charge at https://simtk.org/home/mdopx and a web portal will be available via http://sysbio.indiana.edu/virusx. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
On perfect Γ‐decompositions of the complete graph
Authors: Buratti Marco , Pasotti Anita
Published: July 2008

Generalizing the well‐known concept of an i‐perfect cycle system, Pasotti [Pasotti, in press, Australas J Combin] defined a Γ‐decomposition (Γ‐factorization) of a complete graph Kv to be i‐perfect if for every edge [x, y] of Kv there is exactly one block of the decomposition (factor of the factorization) in which x and y have distance i. In particular, a Γ‐decomposition (Γ‐factorization) of Kv that is i‐perfect for any i not exceeding the diameter of a connected graph Γ will be said a Steiner (Kirkman) Γ‐system of order v. In this article we first observe that as a consequence of the deep theory on decompositions of edge‐colored graphs developed by Lamken and Wilson [Lamken and Wilson, 2000, J Combin Theory Ser A 89, 149–200], there are infinitely many values of v for which there exists an i‐perfect Γ‐decomposition of Kv provided that Γ is an i‐equidistance graph, namely a graph such that the number of pairs of vertices at distance i is equal to the number of its edges. Then we give some concrete direct constructions for elementary abelian Steiner Γ‐systems with Γ the wheel on 8 vertices or a circulant graph, and for elementary abelian 2‐perfect cube‐factorizations. We also present some recursive constructions and some results on 2‐transitive Kirkman Γ‐systems. © 2008 Wiley Periodicals, Inc. J Combin Designs 17: 197–209, 2009
PML/RARα fusion protein mediates the unique sensitivity to arsenic cytotoxicity in acute promyelocytic leukemia cells: Mechanisms involve the impairment of cAMP signaling and the aberrant regulation of NADPH oxidase
Authors: Li Lingna , Wang Jie , Ye Richard D. , Shi Guiying , Jin Huifang , Tang Xueming , Yi Jing
Published: July 2008

Acute promyelocytic leukemia (APL) cells are characterized by PML/RARα fusion protein, high responsiveness to arsenic trioxide (ATO)‐induced cytotoxicity and an abundant generation of reactive oxygen species (ROS). In this study we investigated the association among these three features in APL‐derived NB4 cells. We found that NADPH oxidase‐derived ROS generation was more abundant in NB4 cells compared with monocytic leukemia U937 cells. By using PR9, a sub‐line of U937 stably transduced with the inducible PML/RARα expression vectors, we attributed disparities on ROS generation and ATO sensitivity to the occurrence of PML/RARα fusion protein, since PML/RARα‐expressing cells appeared higher NADPH oxidase activity, higher ROS level and higher sensitivity to ATO. On the other hand, the basal intensity of cAMP signaling pathway was compared between NB4 and U937 as well as between PR9 cells with or without PML/RARα, demonstrating that PML/RARα‐expressing cells had an impaired cAMP signaling pathway which relieved its inhibitory effect on NADPH oxidase derived ROS generation. In summary, the present study demonstrated the correlation of PML/RARα with cAMP signaling pathway, NADPH oxidase and ROS generation in APL cells. PML/RARα that bestows NB4 cells various pathological features, paradoxically also endows these cells with the basis for susceptibility to ATO‐induced cytotoxcity. J. Cell. Physiol. 217: 486–493, 2008. © 2008 Wiley‐Liss, Inc.
Shear stress‐induced Ets‐1 modulates protease inhibitor expression in microvascular endothelial cells
Authors: Milkiewicz Malgorzata , Uchida Cassandra , Gee Eric , Fudalewski Tomasz , Haas Tara L.
Published: July 2008

Elevated shear stress within the skeletal muscle microvasculature is implicated in the induction of a longitudinal splitting form of angiogenesis, which is characterized by the lack of basement membrane breakage. We investigated whether the transcriptional regulator, Ets‐1, is responsive to changes in hemodynamic forces and if so, whether Ets‐1 controls microvascular endothelial cell integrity by inducing the expression of inhibitors of matrix degrading proteases. Rats were treated with prazosin for 2, 4, and 7 days to increase in microvascular shear stress in hindlimb skeletal muscles. In complimentary in vitro experiments, rat microvascular skeletal muscle endothelial cells were exposed to laminar shear stress (15 dyne/cm2) for 0.5, 2, and 24 h. TaqMan PCR analysis of laser microdissected capillaries isolated from EDL muscles demonstrated transient (after 2 days) induction of Ets‐1 gene expression. In cultured cells, a transient up‐regulation of Ets‐1 mRNA was observed after 2 h shear stimulation, accompanied by increased phosphorylation of Ets‐1 and enhanced Ets‐1 DNA binding activity. This response was modulated by ERK1/2 and p38 MAP kinases, but was not dependent on NOS or COX‐2 activity. PAI‐1, TIMP‐1 and TIMP‐3 mRNA were elevated significantly in prazosin treated EDL, and in response to shear stimulation in vitro. In cultured endothelial cells, Ets‐1 RNA interference abolished the shear‐induced increases in Ets‐1, PAI‐1, TIMP‐1, and TIMP‐3 mRNA expression. These results suggest that enhanced laminar shear stress may act to preserve the integrity of microvascular walls in part through Ets‐1‐dependent induction of protease inhibitors. J. Cell. Physiol. 217: 502–510, 2008. © 2008 Wiley‐Liss, Inc.
Role of the hemopexin domain of matrix metalloproteinases in cell migration
Authors: Dufour Antoine , Sampson Nicole S. , Zucker Stanley , Cao Jian
Published: July 2008

The biological functions of matrix metalloproteinases (MMPs) extend beyond extracellular matrix degradation. Non‐proteolytic activities of MMPs are just beginning to be understood. Herein, we evaluated the role of proMMPs in cell migration. Employing a Transwell chamber migration assay, we demonstrated that transfection of COS‐1 cells with various proMMP cDNAs resulted in enhancement of cell migration. Latent MMP‐2 and MMP‐9 enhanced cell migration to a greater extent than latent MMP‐1, ‐3, ‐11 and ‐28. To examine if proteolytic activity is required for MMP‐enhanced cell migration, three experimental approaches, including fluorogenic substrate degradation assay, transfection of cells with catalytically inactive mutant MMP cDNAs, and addition of hydroxamic acid‐derived MMP inhibitors, were employed. We demonstrated that the proteolytic activities of MMPs are not required for MMP‐induced cell migration. To explore the mechanism underlying MMP‐enhanced cell migration, structure‐function relationship of MMP‐9 on cell migration was evaluated. By using a domain swapping approach, we demonstrated that the hemopexin domain of proMMP‐9 plays an important role in cell migration when examined by a transwell chamber assay and by a phagokinetic migration assay. TIMP‐1, which interacts with the hemopexin domain of proMMP‐9, inhibited cell migration, whereas TIMP‐2 had no effect. Employing small molecular inhibitors, MAPK and PI3K pathways were found to be involved in MMP‐9‐mediated cell migration. In conclusion, we demonstrated that MMPs utilize a non‐proteolytic mechanism to enhance epithelial cell migration. We propose that hemopexin homodimer formation is required for the full cell migratory function of proMMP‐9. J. Cell. Physiol. 217: 643–651, 2008. © 2008 Wiley‐Liss, Inc.
Time‐domain simulation of electromagnetic wave propagation in two‐level dielectrics
Authors: Paul J. , Christopoulos C. , Thomas D. W. P.
Published: July 2008

A method for the time‐domain simulation of electromagnetic wave propagation in two‐level dielectric media is developed. The technique involves using transmission‐line modelling (TLM) and 𝒵‐transform methods to develop an algorithm to simulate the Maxwell–Bloch equations. The approach is accurate and free from numerical instabilities. The scheme was validated for the small‐signal case by demonstration of the correspondence principle with the classical Lorentz oscillator. Results obtained for propagation in the two‐level medium are in agreement with previous studies in the literature. In addition, results are shown demonstrating gain, self‐induced transparency (SIT), Rabi flopping and laser oscillations. Copyright © 2008 John Wiley & Sons, Ltd.
Microstrip antenna analysis using the method of fundamental solutions
Authors: Sensale‐Rodriguez Berardi , Sensale Berardi , Leitão Vitor M. A. , Peixeiro Custódio
Published: July 2008

The method of fundamental solutions (MFS) is proposed for the analysis of microstrip patch antennas of arbitrary shape. The MFS consists mainly in approximating the solution of a problem by a linear combination of known fundamental solutions associated with source points located outside the domain. The implementation of the MFS is simple and computationally efficient. Simulation results are obtained for rectangular, circular and triangular microstrip patch antennas. The resonance frequency and input impedance results are in good agreement with those published in the literature. Two prototypes have been fabricated and tested. Good agreement has been obtained between the MFS simulations and the experimental results. Copyright © 2008 John Wiley & Sons, Ltd.
Food and feed components for gut health‐promoting adhesion of E. coli and Salmonella enterica
Authors: Becker Petra M , Galletti Sara
Published: July 2008

BACKGROUND: A host runs less risk of contracting a gastrointestinal infection when enteropathogenic bacteria adhere to dietary fibers instead of to epithelial cell receptors. The aim of this study was to test the binding capacity of food and feed components for intestinal bacteria from various hosts using a miniaturized in vitro assay. In total, 18 dietary components were tested with four strains of E. coli, seven strains of Salmonella enterica and two strains of Lactobacillus.

RESULTS: A comparison of the results obtained for all Salmonella strains tested revealed that konjac gum and sesame seed extract represented the most efficient binding matrices. Similarly, for all E. coli strains tested, sesame seed extract and artichoke performed well as binding matrices. Salmonella isolates from chickens adhered best to sesame seed extract. E. coli K88 and S. enterica sv. Typhimurium isolated from pigs effectively bound to BioMos®, pumpkin, sesame seed extract, and tomato. Sesame seed extract and tomato also had adhesive capacities for E. coli K 99, S. enterica sv. Dublin, and S. enterica sv. Typhimurium from calves. With human isolates, konjac gum showed a high binding potential for S. enterica and E. coli.

CONCLUSION: The adhesion screening of different food and feed components resulted in highly discriminating product rankings. Copyright © 2008 Society of Chemical Industry
Experimental measurements and theoretical calculations of the chemical shifts and coupling constants of three azines (benzalazine, acetophenoneazine and cinnamaldazine)
Authors: Silva Artur M. S. , Sousa Regina M. S. , Jimeno María Luisa , Blanco Fernando , Alkorta Ibon , Elguero José
Published: July 2008

Three azines, two of them doubly labeled with 15N, have been studied by multinuclear magnetic resonance in solution and in the solid state. The spectral parameters obtained by iterative analyses have been compared with DFT/B3LYP calculated values (absolute shieldings and coupling constants). The agreement is generally good. Some anomalies have been discussed in relation to the structure of these compounds. Copyright © 2008 John Wiley & Sons, Ltd.
Improving accuracy and efficiency of blind protein‐ligand docking by focusing on predicted binding sites
Authors: Ghersi Dario , Sanchez Roberto
Published: July 2008

The use of predicted binding sites (binding sites calculated from the protein structure alone) is evaluated here as a tool to focus the docking of small molecule ligands into protein structures, simulating cases where the real binding sites are unknown. The resulting approach consists of a few independent docking runs carried out on small boxes, centered on the predicted binding sites, as opposed to one larger blind docking run that covers the complete protein structure. The focused and blind approaches were compared using a set of 77 known protein‐ligand complexes and 19 ligand‐free structures. The focused approach is shown to: (1) identify the correct binding site more frequently than blind docking; (2) produce more accurate docking poses for the ligand; (3) require less computational time. Additionally, the results show that very few real binding sites are missed in spite of focusing on only three predicted binding sites per target protein. Overall the results indicate that, by improving the sampling in regions that are likely to correspond to binding sites, the focused docking approach increases accuracy and efficiency of protein ligand docking for those cases where the ligand‐binding site is unknown. This is especially relevant in applications such as reverse virtual screening and structure‐based functional annotation of proteins. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The mechanism of amyloid‐fibril formation by stefin B: Temperature and protein concentration dependence of the rates
Authors: Škerget Katja , Vilfan Andrej , Pompe‐Novak Maruša , Turk Vito , Waltho Jonathan P. , Turk Dušan , Žerovnik Eva
Published: July 2008

Cystatins, a family of structurally related cysteine proteinase inhibitors, have proved to be useful model system to study amyloidogenesis. We have extended previous studies of the kinetics of amyloid‐fibril formation by human stefin B (cystatin B) and some of its mutants, and proposed an improved model for the reaction. Overall, the observed kinetics follow the nucleation and growth behavior observed for many other amyloidogenic proteins. The minimal kinetic scheme that best fits measurements of changes in CD and thioflavin T fluorescence as a function of protein concentration and temperature includes nucleation (modeled as NI irreversible transitions with equivalent rates (kI), which fitted with NI = 64), fibril growth and nonproductive oligomerization, best explained by an off‐pathway state with a rate‐limiting escape rate. Three energies of activation were derived from global fitting to the minimal kinetic scheme, and independently through the fitting of the individual component rates. Nucleation was found to be a first‐order process within an oligomeric species with an enthalpy of activation of 55 ± 4 kcal mol−1. Fibril growth was a second‐order process with an enthalpy of activation (27 ± 5 kcal mol−1), which is indistinguishable from that of tetramer formation by cystatins, which involves limited conformational changes including proline trans to cis isomerization. The highest enthalpy of activation (95 ± 5 kcal mol−1 at 35°C), characteristic of a substantial degree of unfolding as observed prior to domain‐swapping reactions, equated with the escape rate of the off‐pathway oligomeric state. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Evaluation of implanted InSb p+n diodes passivated with composite anodic oxide/SiOxstack
Authors: Liu K. C. , Luo J. J. , Dai L. K.
Published: July 2008

This investigation presents detailed characteristics of an implanted planar InSb p+n diode with a junction area scaled down to 20 × 20 μm2. Low‐temperature photo‐chemical vapor deposition oxide stacked with an optimized thin anodic film, instead of a gate control structure, is used to control the planar surface potential of the implanted p+n diode under the weak inversion condition on the n‐type surface and under weak accumulation on the p‐type surface. The zero‐bias resistance–area product is 7.6 × 104Ω cm2at 77 K. To the best of the authors' knowledge, this result represents the best performance of a small‐area and implanted planar diode to date. The dark current is controlled by an internal shunt conduction mechanism, which seems to be related to the defects that are produced by the implantation. Low leakage current and high breakdown voltage have proven the feasibility of the composite anodic oxide/SiOxthat is stacked as the passivation structure in small‐pixel InSb p+n photodiodes for focal plane array applications. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Switching thresholds in MTJ using SPICE model – Effects of spin and Ampere torques
Authors: Malathi M. , Prabhakar A.
Published: July 2008

Spin torque due to spin polarized tunneling current can be used to switch the free layer in a magnetic tunnel junction (MTJ). This current also gives rise to an Ampere torque, which influences the switching threshold of the MTJ. We modified the Landau–Lifschitz–Gilbert equation (LLGE) to include an Ampere torque term and solved for the magnetization dynamics under the single domain approximation using a linear solver in SPICE. We also extend the model to a square array of MTJs to study the effect of nearest neighbour interactions in addition to effects like demagnetization and magnetostatic interactions with the pinned layer. The interlayer exchange field between the free and pinned layers of a MTJ and the spin torque are competing factors that decide the threshold current density for switching the MTJ. We used a two current model to study the effects of barrier height and barrier thickness on spin torque and exchange energy. We observe that both the spin torque and exchange energy decrease with an increase in barrier height (for ferromagnetic coupling) and barrier thickness. We find that the inclusion of Ampere torque causes a reduction in the switching current. Varying the thickness of MgO and Al2O3 barriers allows us to minimize the switching threshold voltage. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preparation, structure and gas‐sensing properties of γ‐Fe2O3 and γ‐Fe2O3–TiO2 thick films
Authors: Rezlescu E. , Doroftei C. , Rezlescu N. , Popa P. D.
Published: July 2008

In this paper, the preparation of γ‐Fe2O3 and γ‐Fe2O3–TiO2 thick films by a screen printing method is presented and their sensitivities and responses to acetone, ethyl alcohol, ammonia and liquefied petroleum gas are studied. The experimental results revealed that the gas sensitivity is strongly related to operating temperature, film composition and gas type. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical transport in boron‐doped polycrystalline zinc oxide thin films
Authors: Steinhauser J. , Faÿ S. , Oliveira N. , Vallat‐Sauvain E. , Zimin D. , Kroll U. , Ballif C.
Published: July 2008

Boron doped Zinc oxide (ZnO:B) thin films are commonly used as transparent conductive oxide (TCO) in thin film silicon solar cells. TCO films with a high electrical conductivity combined with a high transparency are required for this application. In this paper, the electronic transport properties in polycrystalline ZnO:B grown by low pressure chemical vapor deposition (LPCVD) were investigated using Hall effect measurements and optical spectroscopy techniques. The systematic comparison between the optical mobility values deduced from the reflectance spectra using the Drude model, and the Hall mobility values, allowed us to clearly separate the respective influences on the electrical transport of potential barrier at grain boundaries and intragrain scattering. By analyzing the results for samples with large variation of grain size and doping level, we observed a continuous transition from grain boundary scattering to intragrain scattering. Finally, the stability of LPCVD ZnO:B in a humid environment was also investigated. The degradation of the electrical film properties due to damp heat treatment is analyzed and discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Indium oxide thin‐film transistor by reactive ion beam assisted deposition
Authors: Vygranenko Y. , Wang K. , Vieira M. , Nathan A.
Published: July 2008

This work reports on the fabrication and characterization of indium oxide semiconducting films and their application in thin‐film transistors (TFTs). The films have been deposited at room temperature by oxygen ion beam assisted e‐beam evaporation. The influence of deposition conditions on film properties including the crystal structure, conductivity, and intrinsic stress is analyzed. It is found that the electrical properties of indium oxide films can be engineered from metallic to insulating and the film structure can be varied from amorphous to microcrystalline by adjusting deposition rate, oxygen ion energy, and ion beam flux. Furthermore, the highly‐resistive films with considerable microstructural crystallinity exhibit n‐type field‐effect behaviour. A field‐effect mobility of 1.4 cm2/V s, and ON/OFF current ratio of ∼106 are observed for transistors with a silicon dioxide gate dielectric. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Novel III‐nitride based transparent photodetectors for standing wave interferometry
Authors: Hauguth S. , Lebedev V. , Mauder Ch. , Niebelschütz F. , Büchner H.‐J. , Jäger G. , Ambacher O.
Published: July 2008

The concept of a standing wave (SW) interferometer has been extensively investigated for the last decade. A key problem within these efforts is the development of a transparent ultra‐thin photodetector for sampling the intensity profile of the generated SW. We report on the simulation and fabrication as well as on the structural and optoelectronical characterization of highly transparent AlGaN/GaN double‐heterostructure and InGaN metal–semiconductor–metal photodetectors based on intraband and band‐to‐band transitions, respectively. Both detectors have a 20 nm thick optically active layer designed for the light absorption at the wavelength of ∼633 nm. Besides good structural properties of both Al0.35Ga0.65N/GaN and In0.56Ga0.44N structures, the absorbance of the InGaN‐based detector was found ∼20 times higher compared to the AlGaN/GaN photodetectors. The temporal characteristics of the detectors are limited by both the RC‐constant and by the persistent photocurrent effect. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanostructuring of an AlGaInP light emitting diode for surface plasmon enhanced emission of light output
Authors: Perks R. M. , Kettle J. , Lalev G. M. , Dimov S.
Published: July 2008

This work describes a successful post fabrication method of applying a plasmonic grating to the surface of a mounted AlGaInP LED device. A Carl Zeiss 1540 XB Focused Ion beam system was used to mill holes in a thin gold layer with a periodicity of around 540 nm. Measurements of the total light output of the device compared with a standard un‐textured device show that the plasmonic grating was found to significantly affect the light output characteristics such that the overall light output was reduced. This is attributed to the fact that only p‐polarised light can interact with the hole array. Furthermore, the onset of saturation in the textured device was not evident as compared with the un‐textured device. This is attributed to improved current spreading in the device due to the top gold layer. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Development and characterization of light‐emitting diodes (LEDs) based on ruthenium complex single layer for transparent displays
Authors: Santos G. , Fonseca F. , Andrade A. M. , Patrocínio A. O. T. , Mizoguchi S. K. , Murakami Iha N. Y. , Peres M. , Monteiro T. , Pereira L.
Published: July 2008

In this work, two ruthenium complexes, [Ru(bpy)3](PF6)2 and [Ru(ph2phen)3](PF6)2 in poly(methylmethacrylate) matrix were employed to build single‐layer light‐emitting electrochemical cells by spin coating on indium tin oxide substrate. In both cases the electroluminescence spectra exhibit a relatively broad band with maxima near to 625 nm and CIE (x, y) color coordinates of (0.64, 0.36), which are comparable with the photoluminescence data in the same medium. The best result was obtained with the [Ru(bpy)3](PF6)2 device where the optical output power approaches 10 µW at the band maximum with a wall‐plug efficiency higher than 0.03%. The lowest driving voltage is about 4 V for an electrical current of 20 mA. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron spin resonance and quantum critical phenomena in VOx multiwall nanotubes
Authors: Demishev S. V. , Chernobrovkin A. L. , Goodilin E. A. , Glushkov V. V. , Grigorieva A. V. , Samarin N. A. , Sluchanko N. E. , Semeno A. V. , Tretyakov Yu. D.
Published: July 2008

Basing on the high frequency (60 GHz) electron spin resonance study of the VOx multiwall nanotubes (VOx ‐NTs) carried out in the temperature range 4.2–200 K we report: (i) the first direct experimental evidence of the presence of the antiferromagnetic dimers in VOx ‐NTs and (ii) the observation of an anomalous low temperature growth of the magnetic susceptibility for quasi‐free spins, which obey the power law χ (T)∼1/T α with the exponent α ≈ 0.6 in a wide temperature range 4.2–50 K. We argue that the observed departures from the Curie–Weiss behaviour manifest the onset of the quantum critical regime and formation of the Griffiths phase as a magnetic ground state of these spin species. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adaptive charting schemes based on double sequential probability ratio tests
Authors: Li Yan , Pu Xiaolong , Tsung Fugee
Published: July 2008

Sequential probability ratio test (SPRT) control charts are shown to be able to detect most shifts in the mean or proportion substantially faster than conventional charts such as CUSUM charts. However, they are limited in applications because of the absence of the upper bound on the sample size and possibly large sample numbers during implementation. The double SPRT (2‐SPRT) control chart, which applies a 2‐SPRT at each sampling point, is proposed in this paper to solve some of the limitations of SPRT charts. Approximate performance measures of the 2‐SPRT control chart are obtained by the backward method with the Gaussian quadrature in a computer program. On the basis of two industrial examples and simulation comparisons, we conclude that the 2‐SPRT chart is competitive in that it is more sensitive and economical for small shifts and has advantages in administration because of fixed sampling points and a proper upper bound on the sample size. Copyright © 2008 John Wiley & Sons, Ltd.
The characterization of selected drugs with infrared laser desorption/tunable synchrotron vacuum ultraviolet photoionization mass spectrometry
Authors: Pan Yang , Yin Hao , Zhang Taichang , Guo Huijun , Sheng Liusi , Qi Fei
Published: July 2008

Some selected drugs including captopril, fudosteine and racecadotril have been analyzed by infrared (IR) laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (PIMS). The molecular ions of captopril and racecadotril are exclusively observed without any fragments at near threshold single‐photon ionization (SPI). However, fudosteine easily forms fragments even at a photon energy near the ionization threshold, indicating the instability of its molecular ion. For these drugs, a number of fragments are yielded with the increase of photon energy. The structures of such fragments proposed by IR LD/VUV PIMS are supported by electron ionization time‐of‐flight mass spectrometry (EI‐TOFMS) results. Fragmentation pathways are discussed in detail. Copyright © 2008 John Wiley & Sons, Ltd.
Gas chromatography flow rates for determining deuterium/hydrogen ratios of natural gas by gas chromatography/high‐temperature conversion/isotope ratio mass spectrometry
Authors: Jia Wanglu , Peng Ping'an , Liu Jinzhong
Published: July 2008

The effects of the gas chromatography flow rate on the determination of the deuterium/hydrogen (D/H) ratios of natural gas utilising gas chromatography/high‐temperature conversion/isotope ratio mass spectrometry (GC/TC/IRMS) have been evaluated. In general, the measured δD values of methane, ethane and propane decrease with increase in column flow rate. When the column flow rate is 1 mL/min or higher, which is commonly used for the determination of D/H ratios of natural gas, the organic H in gas compounds may not be completely converted into hydrogen gas. Based on the results of experiments conducted on a GC column with an i.d. of 0.32 mm, a GC flow rate of 0.6 mL/min is proposed for determining the D/H ratios of natural gas by GC/TC/IRMS. Although this value may be dependent on the instrument conditions used in this work, we believe that correct δD values of organic compounds with a few carbon atoms are obtained only when relatively low GC flow rates are used for D/H analysis by GC/TC/IRMS. Moreover, as the presence of trace water could significantly affect the determination of D/H ratios, a newly designed inlet liner was used to remove trace water contained in some gas samples. Copyright © 2008 John Wiley & Sons, Ltd.
A laboratory comparison of two methods used to estimate the isotopic composition of soil δ13CO2 efflux at steady state
Authors: Kayler Zachary E. , Sulzman Elizabeth W. , Marshall John D. , Mix Alan , Rugh William D. , Bond Barbara J.
Published: July 2008

The stable isotopic composition of soil 13CO2 flux is important for monitoring soil biological and physical processes. While several methods exist to measure the isotopic composition of soil flux, we do not know how effective each method is at achieving this goal. To provide clear evidence of the accuracy of current measurement techniques we created a column filled with quartz sand through which a gas of known isotopic composition (−34.2‰) and concentration (3000 ppm) diffused for 7 h. We used a static chamber at equilibrium and a soil probe technique to test whether they could identify the isotopic signature of the known gas source. The static chamber is designed to identify the source gas isotopic composition when in equilibrium with the soil gas, and the soil probe method relies on a mixing model of samples withdrawn from three gas wells at different depths to identify the gas source. We sampled from ports installed along the side of the sand column to describe the isotopic and concentration gradient as well as to serve as a control for the soil probe. The soil probe produced similar isotopic and concentration values as the control ports, as well as Keeling intercepts. The static chamber at equilibrium did not identify the source gas but, when applied in a two end‐member mixing model, did produce a similar Keeling intercept produced from the control ports. Neither of the methods was able to identify the source gas via the Keeling plot method probably because CO2 profiles did not reach isotopic steady state. Our results showed that the static chamber at equilibrium should be used only with a Keeling plot approach and that the soil probe is able to provide estimates of uncertainty for the isotopic composition of soil gas as well as information pertinent to the soil profile. Copyright © 2008 John Wiley & Sons, Ltd.
The patch mosaic of an old‐growth warm‐temperate forest: patch‐level descriptions of 40‐year gap‐forming processes and community structures
Authors: Manabe Tohru , Shimatani Kenichiro , Kawarasaki Satoko , Aikawa Shin‐Ichi , Yamamoto Shin‐Ichi
Published: July 2008

Old‐growth forests consist of various types of small patches that reflect their own gap‐forming process, which includes changes in environmental conditions occurring over several decades. We reconstructed the gap‐forming processes that had occurred during a 40‐year period for eight representative patches of an old‐growth evergreen broad‐leaved forest in Japan, and examined the current community structure. The selected patches were based on (1) changes in canopy heights estimated from aerial photographs taken in four different years, (2) long‐term ecological research (LTER) monitoring records, and (3) a recent field survey, so that they sufficiently covered characteristic gap‐forming processes such as a new gap, an old gap and consistently closed canopy. Height and diameter at breast height (DBH) were measured on all living trees taller than 1.3 m. In their height distributions, currently almost closed patches that were open in 1966 show a rotated sigmoid, whereas their DBH distributions are an inverse J‐shape. In contrast, patches that have been consistently under a closed canopy exhibit gentle inverse J‐shapes for both distributions. For species composition, there are no clear contrasts associated with the past gap‐forming processes except for the existence of fast‐growing deciduous species in large currently open patches. Our results suggested that the variation in several decades of gap‐forming processes played a central role in the high patch diversity and the complex patch mosaic of the forest. Diverse gap‐forming processes created micro‐environmental heterogeneity both vertically and horizontally, and contributed to the maintenance of the species‐rich, warm‐temperate old‐growth forest.
An Improved Method for Separating Cardiolipin by HPLC
Authors: Barceló‐Coblijn Gwendolyn , Murphy Eric J.
Published: July 2008

Herein we report an improved method to separate cardiolipin (Ptd2Gro) from tissue total lipid extracts using a biphasic solvent system combined with high performance liquid chromatography. This method uses a normal phase silica column and two mobile phases: mobile phase A that was n‐hexane:2‐propanol (3:2 by vol) and mobile phase B that was n‐hexane:2‐propanol:water (56.7:37.8:5.5 by vol). The initial solvent conditions were 95% A and 5% B, with a flow rate of 1.5 mL/min. The samples were from non‐derivatized aliquots of liver, heart, or brain lipid extracts. The peak corresponding to Ptd2Gro appeared at 31 min, was well defined and did not overlap with neighboring peaks. The adjacent peak corresponded to ethanolamine glycerophospholipids and the remaining phospholipids were eluted in a single peak. The identity of the phospholipids separated by this method was verified by thin layer chromatography (TLC) and fatty acid analysis, which confirmed that the Ptd2Gro was well resolved from other phospholipids. This method is useful to separate and quantify Ptd2Gro from small tissue samples thereby avoiding the variability associated with TLC methods.
18O Labeling for a Quantitative Proteomic Analysis of Glycoproteins in Hepatocellular Carcinoma
Authors: Chaerkady Raghothama , Thuluvath Paul J. , Kim Min-Sik , Nalli Anuradha , Vivekanandan Perumal , Simmers Jessica , Torbenson Michael , Pandey Akhilesh
Published: July 2008

Introduction

Quantitative proteomics using tandem mass spectrometry is an attractive approach for identification of potential cancer biomarkers. Fractionation of complex tissue samples into subproteomes prior to mass spectrometric analyses increases the likelihood of identifying cancer-specific proteins that might be present in low abundance. In this regard, glycosylated proteins are an interesting class of proteins that are already established as biomarkers for several cancers.

Materials and Methods

In this study, we carried out proteomic profiling of tumor and adjacent non-cancer liver tissues from hepatocellular carcinoma (HCC) patients. Glycoprotein enrichment from liver samples using lectin affinity chromatography and subsequent18O/16O labeling of peptides allowed us to obtain relative abundance levels of lectin-bound proteins. As a complementary approach, we also examined the relative expression of proteins in HCC without glycoprotein enrichment. Lectin affinity enrichment was found to be advantageous to quantitate several interesting proteins, which were not detected in the whole proteome screening approach. We identified and quantitated over 200 proteins from the lectin-based approach. Interesting among these were fetuin, cysteine-rich protein 1, serpin peptidase inhibitor, leucine-rich alpha-2-glycoprotein 1, melanoma cell adhesion molecule, and heparan sulfate proteoglycan-2. Using lectin affinity followed by PNGase F digestion coupled to18O labeling, we identified 34 glycosylation sites with consensus sequence N-X-T/S. Western blotting and immunohistochemical staining were carried out for several proteins to confirm mass spectrometry results.

Conclusion

This study indicates that quantitative proteomic profiling of tumor tissue versus non-cancerous tissue is a promising approach for the identification of potential biomarkers for HCC.
NF‐κB‐dependency and consequent regulation of IL‐8 in echinomycin‐induced apoptosis of HT‐29 colon cancer cells
Authors: Park Ju Youn , Chang Jae‐Ho , Bae Keum Seok , Lee Kyoung Ho , Choi Sun Ju , Park Joo Young , Ryang Yong Suk , Kim Soo‐Ki
Published: July 2008

The present study was to see whether echinomycin‐induced apoptosis would be NF‐κB‐dependent and if so, whether echinomycin would activate or inhibit NF‐κB as well as resultant chemokine IL‐8 expression. In HT‐29 cells echinomycin activated NF‐κB in time‐dependent manner. EMSA in the presence of antibodies specific for p50 and p65 subunits indicated that echinomycin‐induces the translocation of p50–p65 heterodimeric subunits of NF‐κB. Levels of IκB were detected at initial echinomycin treatment and thereafter decreased, faintly seen after a 6 h treatment. In contrast p‐IκB levels were clearly detected throughout 6–24 h of echinomycin treatment, albeit initially fainted. To clarify the role of NF‐κB on IL‐8 expression in echinomycin‐mediated apoptosis of HT‐29 cells, ELISA plus RT‐PCR clearly showed that IL‐8 production is inducible by echinomycin treatment. Using a specific inhibitor, IL‐8 regulation at echinomycin treatment in HT‐29 cells occurred via both caspase‐3 and NF‐κB‐dependent signal pathway. To confirm whether two different pathways (NF‐κB and caspase) would be coupled, only NF‐κB inhibitor (PDTC) and caspase‐3 specific inhibitor (Z‐DEVD‐FMK) together significantly attenuated echinomycin‐initiated apoptosis of HT‐29 cells, pretreatment of HT‐29 cells with PDTC rarely affected echinomycin‐induced caspase‐3 activation. So echinomycin‐induced apoptosis in HT‐29 cells occurs via NF‐κB activation independent of caspase‐3 activation modulating the resultant‐linked key chemokine IL‐8 expression and echinomycin‐induced apoptosis is NF‐κB‐dependant and directly related to NF‐κB activation, consequently regulating IL‐8 expression.
Interactions between the budding yeast IQGAP homologue Iqg1p and its targets revealed by a split‐EGFP bimolecular fluorescence complementation assay
Authors: Pathmanathan Sevvel , Barnard Emma , Timson David J.
Published: July 2008

A split‐EGFP based bimolecular fluorescence complementation (BiFC) assay has been used to detect interactions between the Saccharomyces cerevisiae cytoskeletal scaffolding protein Iqg1p and three targets: myosin essential light chain (Mlc1p), calmodulin (Cmd1p) and the small GTPase Cdc42p. The format of the BiFC assay used ensures that the proteins are expressed at wild type levels thereby avoiding artefacts due to overexpression. This is the first direct in vivo detection of these interactions; in each case, the complex is localised to discrete regions of the yeast cytoplasm. The labelling with EGFP fragments results in changes in growth kinetics, cell size and budding frequency. This is partly due to the reassembled EGFP locking the complexes into essentially permanent interactions. The consequences of this for Iqg1p interactions and BiFC assays in general are discussed.
Chronic pain and other sequelae in long‐term breast cancer survivors: Nationwide survey in Denmark
Authors: Peuckmann V. , Ekholm O. , Rasmussen N.K. , Groenvold M. , Christiansen P. , Møller S. , Eriksen J. , Sjøgren P.
Published: July 2008

Objectives: To investigate self‐reported chronic pain and other sequelae in a nationally representative sample of long‐term breast cancer survivors (BCS).

Design: Age‐stratified random sample of 2,000 female BCS ≥ 5 years after primary surgery without recurrence drawn from the Danish Breast Cancer Cooperative Group register, which is representative regarding long‐term BCS in Denmark.

Assessment: Self‐administered questionnaire including questions on sociodemography, chronic pain (≥6 months), health‐related quality of life (HRQOL) and other sequelae related to breast cancer. Associations with treatment were investigated. Report of chronic pain was compared to normative data.

Results: The response rate was 79%. Chronic pain prevalence of 42% was significantly higher in BCS compared to general population women (SRR: 1.32; 95% CI: 1.23–1.42). Sequelae related to breast cancer were paraesthesia 47%, chronic pain 29%, arm/shoulder swelling 25%, phantom sensations 19%, and allodynia 15%. Chronic pain related to breast cancer was significantly associated with poorer HRQOL and higher medicine consumption, and, in multiple logistic regression analysis, with age (<70 years), short education, being single (divorced, widowed, separated), radiotherapy, and time since operation <10 years. Radiotherapy and younger age were significantly associated with most sequelae.

Conclusion: Chronic pain was more prevalent in BCS compared to the general population. Significant predictors for sequelae related to breast cancer were radiotherapy and younger age. Future research should therefore prioritize sequelae prevention.
Prenatal exposure to a non‐steroidal anti‐inflammatory drug or saline solution impairs sciatic nerve morphology: a stereological and histological study
Authors: Canan Sinan , Aktaş Abit , Ulkay M. Basak , Colakoglu Serdar , Ragbetli Murat Cetin , Ayyildiz Mustafa , Geuna Stefano , Kaplan Suleyman
Published: July 2008

The toxic effect of non‐steroidal anti‐inflammatory drugs (NSAIDs) during development has been widely investigated. While it has been shown that these drugs impair central nervous development and compromise the neural activity, the effects of these substances on the development of peripheral nerves are still not clarified. In the present study, sciatic nerves withdrawn from three experimental groups of 4‐week‐old rats, prenatally exposed to either saline solution, or diclofenac sodium, and controls not exposed to any substance, were evaluated in terms of axon number, cross‐sectional area of axon and myelin sheet thickness as well as of the ultrastructure of nerve fibers. Comparisons of stereological estimations among these three groups showed that axon number and mean axon cross‐sectional area, but not average myelin sheet thickness, were significantly decreased in rats that were exposed to both diclofenac sodium and also to the saline solution, in comparison of the control group. Electron microscope analysis revealed, in both treated groups, deterioration of myelin sheaths that was more pronounced in rats that were exposed to diclofenac sodium. Altogether, these findings show that the prenatal administration of both diclofenac sodium and saline solution impairs peripheral nervous system development, thus suggesting that this potential teratogenic effect should be also taken into consideration in the clinical use of these substances in pregnant patients.
Clinical and metabolic effects of medroxyprogesterone acetate and ethinyl estradiol plus drospirenone in women with polycystic ovary syndrome
Authors: Özdemir Suna , Görkemli Hüseyin , Gezginç Kazim , Özdemir Mustafa , Kiyici Aysel
Published: July 2008

Objectives: To investigate the effects of treatment with medroxyprogesterone acetate (MPA), 10 days per month for 6 months, on lipid and carbohydrate metabolism in women with polycystic ovary syndrome (PCOS). Methods: Sixty‐three women with PCOS were randomized to receive MPA or ethinyl estradiol plus drospirenone. Results: There were no changes in lipid or carbohydrate metabolism in the MPA group, but serum levels of luteinizing hormone (P < 0.001) and total testosterone (P < 0.003) significantly decreased, as did the free androgen index (P < 0.02) and acne (P < 0.03) and seborrhea (P < 0.04) scores. In the ethinyl estradiol plus drospirenone group lipid and hormone values significantly increased whereas acne, seborrhea, hair loss, and Ferriman‐Gallwey scores decreased. There was no statistically significant change in the total cholesterol to high‐density cholesterol ratio in either group. Conclusion: Treatment of PCOS patients with MPA provided good menstrual cycle control, beneficial changes in hormonal values associated with hyperandrogenism, and no significant changes in lipid or carbohydrate metabolism.
Human defensins and cytokines in vaginal lavage fluid of women with bacterial vaginosis
Authors: Fan S.R. , Liu X.P. , Liao Q.P.
Published: July 2008

Objective

To measure the concentrations of interferon gamma (IFN‐γ), interleukin (IL)‐2, IL‐4, IL‐5, human β‐defensin 2 (HBD‐2), and human defensin 5 (HD‐5) in the vaginal lavage fluid (VLF) of healthy women and women with bacterial vaginosis (BV).

Methods

VLF samples were obtained from 73 women with BV, 15 women with intermediate vaginal flora, 33 healthy women with vaginal pH greater than or equal to 4.5, and a control group of 39 healthy women with vaginal pH less than 4.5. The concentrations of IFN‐γ, IL‐2, IL‐4, IL‐5, HBD‐2, and HD‐5 were measured using enzyme‐linked immunosorbent assay kits.

Results

Concentrations of HBD‐2 and HD‐5 in the VLF of women with BV were significantly higher than in the control group (P < 0.05). IL‐4 concentration was significantly lower in the VLF of women with BV than in the control group (P < 0.05).

Conclusions

HBD‐2 and HD‐5 may be involved in defending against invasion by BV‐related microorganisms and the decrease in IL‐4 concentration may increase susceptibility to BV.