bluuebunny/crossref_metadata_2025 huggingface dataset:
Extended state‐space time integration with high‐frequency energy dissipation
Authors: Krenk Steen
Published: July 2007

The introduction of algorithmic dissipation into conservative time integration algorithms is addressed in two steps. The problem is formulated in state‐space, and it is demonstrated that the use of two balanced dissipation terms—one in the equation of motion and the other in the relation between the state‐space variables—can produce dissipation that increases monotonically with the modal frequency. This formulation is only partially satisfactory, because it leads to dissipation also in the low‐frequency range. A substantially improved form of algorithmic dissipation is then developed by representing the two balanced dissipation terms via auxiliary state‐space variables related to the displacement and velocity increments by a first‐order filter. The filter technique retains the high‐frequency behavior of the original balanced algorithm, but reduces the low‐frequency dissipation from first order in the frequency to third order. Energy balance equations are derived, and the behavior of the two algorithms is described by detailed spectral analysis with explicit asymptotic results directly in terms of the damping parameter of the algorithms. Both algorithms satisfy full symmetry of displacement and normalized velocity variables for the free algorithmically damped vibration of any single mode and, therefore, exhibit monotonic transients without ‘overshoot’ effects. It is also demonstrated how the algorithm can be arranged in ‘single solve’ format, where only the displacement update requires a matrix equation solution, while the velocity and the auxiliary state‐space variables are updated subsequently in each time step by simple vector relations with scalar coefficients. Copyright © 2007 John Wiley & Sons, Ltd.
Least‐squares mixed finite element methods for the RLW equations
Authors: Gu Haiming , Chen Ning
Published: July 2007

A least‐squares mixed finite element (LSMFE) schemes are formulated to solve the 1D regularized long wave (RLW) equations and the convergence is discussed. The L2 error estimates of LSMFE methods for RLW equations under the standard regularity assumption on the finite element partition are given.© 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
Proteome map of normal rat retina and comparison with the proteome of diabetic rat retina: New insight in the pathogenesis of diabetic retinopathy
Authors: Quin Godfrey (Goff) J. , Len Alice C. L. , Billson Frank A. , Gillies Mark C.
Published: July 2007

We have employed proteomics to establish a proteome map of the normal rat retina. This baseline map was then used for comparison with the early diabetic rat retinal proteome. Diabetic rat retinae were obtained from Dark Agouti rats after 10 wk of streptozotocin‐induced hyperglycaemia. Extracted proteins from normal and diabetic rat retinae were separated and compared using 2‐DE. A total of 145 protein spots were identified in the normal rat retina using MALDI‐MS and database matching. LC‐coupled ESI‐MS increased the repertoire of identified proteins by 23 from 145 to 168. Comparison with early diabetic rat retinae revealed 24 proteins unique to the diabetic gels, and 37 proteins absent from diabetic gels. Uniquely expressed proteins identified included the HSPs 70.1A and 8, and platelet activating factor. There were eight spots with increased expression and 27 with decreased expression on diabetic gels. Beta catenin, phosducin and aldehyde reductase were increased in expression in diabetes whilst succinyl coA ligase and dihydropyrimidase‐related protein were decreased. Identification of such changes in protein expression has given new insights and a more comprehensive understanding of the pathogenesis of diabetic retinopathy, widening the scope of potential avenues for new therapies for this common cause of blindness.
Simulated hyperglycemia in rat cardiomyocytes: A proteomics approach for improved analysis of cellular alterations
Authors: Warda Mohamad , Kim Hyoung Kyu , Kim Nari , Youm Jae Boum , Kang Sung Hyun , Park Won Sun , Khoa Tran Min , Kim Young Hwan , Han Jin
Published: July 2007

Diabetic hyperglycemia can lead to stress‐related cellular apoptosis of cardiac tissue. However, the mechanism by which hyperglycemia inflicts this damage on the structure and function of the heart is unclear. In this study, we examined the relationship between proteome alterations, mitochondrial function, and major biochemical and electrophysiological changes affecting cardiac performance during simulated short‐term hyperglycemia. Two‐dimensional comparative proteomics analysis of rat hearts perfused with glucose at high (30 mM) or control (5.5 mM) levels revealed that glucose loading alters cardiomyocyte proteomes. It increased expression levels of initial enzymes of the tricarboxylic acid cycle, and of enzymes of fatty acid β‐oxidation, with consequent up‐regulation of enzymes of mitochondrial electron transport. It also markedly decreased expression of enzymes of glycolysis and the final steps of the tricarboxylic acid cycle. Glucose loading increased the rate of Bax‐independent apoptosis. High glucose increased the duration of the action potential and elevated level of intracellular cytoplasmic calcium. Surprisingly, glucose loading did not influence levels of nitric oxide or mitochondrial superoxide in isolated cardiomyocytes. In summary, short‐term simulated hyperglycemia attenuated expression of many anti‐apoptotic proteins. This effect was apparently mediated via alterations in multiple biochemical pathways that collectively increased apoptotic susceptibility.
Psychometric properties of the Nine‐Item Chinese Patient Satisfaction Questionnaire (ChPSQ‐9) in Chinese patients with hepatocellular carcinoma
Authors: Wong Wing S. , Fielding Richard , Wong Chit Ming , Hedley Anthony J.
Published: July 2007

Patient‐centered approaches to health‐care delivery have increased interest in patient satisfaction with care. However, there is no instrument currently available which takes into account the specific concerns of Chinese patients. This study aimed to evaluate the psychometric properties of the Nine‐Item Chinese Patient Satisfaction Questionnaire (ChPSQ‐9) in a Chinese hepatocellular carcinoma (HPC) sample. A total of 222 Chinese patients with primary HPC completed the ChPSQ‐9, the Medical Interview Satisfaction Scale (MISS), and eating satisfaction measures. The principal component analysis yielded two factors in the ChPSQ‐9, named ‘doctor’ and ‘nurse’ subscales, which explained 79% of the total variance. The instrument also possessed good internal consistency (Cronbach α = 0.93) and concurrent validity with MISS. The divergent validity was indicated by inverse relationships between the ChPSQ‐9 and eating satisfaction. The current results support the use of the ChPSQ‐9 as a self‐report measure of patient satisfaction among Chinese HPC populations and suggest that a caring orientation was highly valued by these patients. Copyright © 2007 John Wiley & Sons, Ltd.
Parental knowledge of fertility in male childhood cancer survivors
Authors: van den Berg Henk , Langeveld Nelia E.
Published: July 2007

Background: In childhood, cancer survivors fertility is a major point of concern. In boys, only semen analysis and impregnation confirm fertility. Since parents constitute a major source of information for children, we investigated recall and assumptions on their child's fertility.

Procedure: One hundred and fifty‐nine families with a boy surviving from cancer were asked for recall and expectations on fertility.

Results: Fifty‐two percent of parents recalled statements on fertility, in 36% this was not so, 12% did not remember. There were no differences for parental gender and age at diagnosis. In case of intensive treatment parents were better informed. After relapse parents were less informed. Nine percent of the parents expected infertility, 60% was uncertain, 31% expected normal fertility.

Conclusions: Based on our and literature findings we conclude that only about half of the parents recalls information on fertility. Lack of information, despite written information, is probably caused by limited oral information provision and defective memorization. One‐third of the parents assumed a normal fertility in their sons. It is highly recommended to check whether parents are adequately informed on fertility at moments they have coped the problems and emotions at initial diagnosis or at relapse, and if needed repeat the information. Copyright © 2007 John Wiley & Sons, Ltd.
Current options in the drug management of nociceptive pain
Authors: Campbell William
Published: July 2007

Strong opioids are commonly used for severe pain and should not be withheld in chronic noncancer pain. Our Drug review considers the properties and efficacy of the various opioids available, followed by an analysis of prescription data, sources of further infor‐mation and the Datafile. Copyright © 2007 Wiley Interface Ltd
Study of the effect of metal ions on hydroxyl–containing molecules
Authors: Kozmutza C. , Bartha F. , Udvardi L. , Varga I.
Published: July 2007

In the framework of the independent particle model the one‐electron properties of the system can be written as the sum of contributions from the individual orbitals. Certain one‐electron energetic quantities could also be attributed to the given orbitals using a convenient partition scheme, such as the method of separated molecular orbitals (SMOs). The one‐electron properties can be derived from localized molecular orbitals (LMOs), too. The aim of this work is to shed light on possible interrelationships between certain SMO and LMO properties of an ‘attacked’ molecular systems and its activity ability. The calculations performed and presented here on the Mg2+ + H2O system in the SMO framework lead to reliable results in comparative studies. Various configurations and basis sets were considered. We investigated the interaction ability between the Mg2+ and Ca2+ ions and the water molecule in terms of first order LMO electric moments. Some calculations in localized representation on the interaction of the phenolic hydroxyl group and of the Mg2+ and the Ca2+ ion have also been carried out. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Enhanced detection of thiol peptides by matrix‐assisted laser desorption/ionization mass spectrometry after selective derivatization with a tailor‐made quaternary ammonium tag containing maleimidyl group
Authors: Li Jun , Ma Huimin , Wang Xiaochun , Xiong Shaoxiang , Dong Suying , Wang Shujuan
Published: July 2007

The goal of this study was to develop a new quaternary ammonium tag for the selective labeling of thiol peptides to improve their detection by using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. The tag, 1‐[3‐(4‐maleimidylphenoxy)propyl]trimethylammonium bromide (MPPTAB), was designed by using the maleimidyl moiety as a selective labeling group for thiols, and a positively charged quaternary ammonium moiety for improving ionization efficiency; the two moieties were combined by a bifunctional linker p‐aminophenol. The properties of the tag were investigated with glutathione as a model peptide, and the derivatization conditions were also optimized with reversed‐phase high‐performance liquid chromatography. The results show that the effective derivatization of thiol peptides can be achieved at the reactant ratio of 3:1 (MPPTAB to the peptide) with a reaction time of 2 h at 37°C, and the excess MPPTAB can be removed with 2‐mercaptoethanol. The comparative study by mass spectrometry indicates that, after derivatization, the signal intensity of thiol peptides with more polar residues such as GPVEDAITAAIGRVAC is increased by 3–5 times, while that with less polar residues like CLLLGGTMV and LCMFVPGYT can be enhanced by more than 100 times. This may be explained in terms of the introduction of the positive charge and the improvement of hydrophobicity: the former raises the ionization efficiency of the tagged peptides, and the latter facilitates their solubility in a hydrophobic matrix, which in turn increases the signal intensity. The present strategy may have a potential use in detecting low‐abundant thiol peptides. Copyright © 2007 John Wiley & Sons, Ltd.
Distinguishing isomeric pyridylaminated high‐mannose (Man7) oligosaccharides based on energy‐resolved mass spectra
Authors: Kurimoto Ayako , Kanie Osamu
Published: July 2007

Analysis of posttranslational modifications of proteins is an important issue for understanding the relationship between protein structure and function. Micro‐scale analytical methods capable of elucidating glycan structures are therefore gaining attention in connection with proteomics research. Recent efforts directed toward this goal have successfully distinguished and in some cases identified glycan structures based on collision‐induced dissociation (CID) analysis. Despite these advancements, the identification of isomeric glycans such as high‐mannose‐type oligosaccharides, Man7GlcNAc2, that are closely related structurally, is not yet possible. Using energy‐resolved mass spectrometry (ERMS), we found that these isomers could be distinguished by comparing the intensities of certain fragment ions. ERMS is useful because the data obtained can be treated quantitatively. Furthermore, it was found that discrimination can be easily achieved by analyzing only the energy‐resolved mass spectra of the sodiated isomeric compounds at the stage of MS2. Thus, the importance and usefulness of ERMS, which provide the factor of activation energy under CID, in analyzing isomeric molecules are clearly shown. Copyright © 2007 John Wiley & Sons, Ltd.
Redox‐dependent formation of disulfide bonds in human replication protein A
Authors: Men Lijie , Roginskaya Marina , Zou Yue , Wang Yinsheng
Published: July 2007

Human replication protein A (RPA) is a single‐stranded DNA (ssDNA)‐binding protein with three subunits. The largest subunit, p70, contains a conserved (cysteine)4‐type zinc‐finger motif that has been implicated in the regulation of DNA replication and repair. Previous studies indicated that the ssDNA‐binding activity of RPA could be redox‐regulated via reversible oxidation of cysteines in the zinc‐finger motif. We exposed recombinant human RPA to hydrogen peroxide and characterized the oxidized protein by liquid chromatography/tandem mass spectrometric (LC/MS/MS) analyses. Our results demonstrated that, upon H2O2 treatment, four cysteines, which reside at the zinc‐finger motif of the p70 subunit, could result in the formation of two pairs of intramolecular disulfides, Cys481‐Cys486 and Cys500‐Cys503; no cysteine sulfinic acid or cysteine sulfonic acid could be found. Moreover, the other 11 cysteines in this protein remained intact. The results demonstrated that the formation of disulfide bonds at the zinc‐finger site was responsible for the redox regulation of the DNA‐binding activity of RPA. Copyright © 2007 John Wiley & Sons, Ltd.
Quantitative Enhanced Raman Scattering of Labeled DNA from Gold and Silver Nanoparticles
Authors: Stokes Robert J. , Macaskill Alexandra , Lundahl P. Johan , Smith W. Ewen , Faulds Karen , Graham Duncan
Published: July 2007

Surface‐enhanced resonance Raman scattering (SERRS) from silver nanoparticles using 514.5‐nm excitation has been shown to offer huge potential for applications in highly sensitive multiplexed DNA assays. If the technique is to be applied to real biological samples and integrated with other methods, then the use of gold nanoparticles and longer wavelengths of excitation are desirable. The data presented here demonstrate that dye‐labeled oligonucleotide sequences can be directly detected by SERRS using gold nanoparticles in a quantitative manner for the first time. The performance of gold and silver nanoparticles as SERRS substrates was assessed using 514.5‐, 632.8‐, and 785‐nm excitation and a range of 13 commercially available dye‐labeled oligonucleotides. The quantitative response allowed the limit of detection to be determined for each case and demonstrates that the technique is highly effective, sensitive, and versatile. The possibility of excitation at multiple wavelengths further enhances the multiplexing potential of the technique. The importance of effectively combining the optical properties of the nanoparticle and the dye label is demonstrated. For example, at 632.8‐nm excitation, the dye BODIPY TR‐X and gold nanoparticles make a strong SERRS combination with very little background fluorescence. This study allows the choice of nanoparticle and dye label for particular experimental setups, and significantly expands the applicability of enhanced Raman scattering for use in many disciplines.
The agile professional culture: A source of agile quality
Authors: Siakas Kerstin V. , Siakas Errikos
Published: July 2007

Ever since agile software development was introduced in the millennium shift, it has become a controversial software engineering topic with practitioners and researchers arguing about the benefits of it. The opinions have been widely divergent, on one side the supporters of the plan‐driven predictable Software Process Improvement (SPI) embracing repeatable processes and continuous improvements, and on the other the agile development putting individuals and interactions over process and tools, working software over comprehensive documentation, customer collaboration over contract negotiation and change response over comprehensive plans.

In this article, the agile methodology is examined from the human and cultural points of view. The concept of culture is analysed for deeper understanding of human and cultural dynamics influencing the agile professional culture. Parallels are drawn to success factors identified in recognised management approaches, such as the Effective Technical and Human Implementation of Computer Systems (ETHICS) and Total Quality Management (TQM).

The type of organisation, suitable to embrace the agile professional development culture, is identified by examining the success factors observed. The democratic type of organisation in the C.HI.D.DI. (Clan‐HIerarchical‐Democratic‐DIsciplined) typology is proposed to be the most suitable to create and sustain added business value and competitive advantage for agile software development. Copyright © 2007 John Wiley & Sons, Ltd.
Transvaginal sonography in the diagnosis of adenomyosis: which findings are most accurate?
Authors: Kepkep K. , Tuncay Y. A. , Göynümer G. , Tutal E.
Published: July 2007

Objectives

To evaluate the accuracy of various transvaginal sonographic findings in adenomyosis by comparing them with histopathological results and to determine the most valuable sonographic feature in the diagnosis of adenomyosis.

Methods

In this prospective study, 70 consecutive patients scheduled for hysterectomy underwent preoperative transvaginal sonography. If at least one of the following sonographic features was present, a diagnosis of adenomyosis was made: heterogeneous myometrial echotexture, globular‐appearing uterus, asymmetrical thickness of the anteroposterior wall of the myometrium, subendometrial myometrial cysts, subendometrial echogenic linear striations or poor definition of the endometrial–myometrial junction. The sonographic features were compared with the histopathological results.

Results

The prevalence of adenomyosis was 37.1% (26/70 patients). The sensitivity, specificity, positive (PPV) and negative (NPV) predictive values and accuracy of transvaginal ultrasound for the diagnosis of adenomyosis were 80.8%, 61.4%, 55.3%, 84.4% and 68.6%, respectively. We found that a regularly enlarged uterus with a globular appearance, subendometrial echogenic linear striations and myometrial cysts had the highest accuracy for the diagnosis of adenomyosis. Of all findings evaluated, heterogeneous myometrium was the most common in patients with adenomyosis (21/26 patients), but it had a poor specificity. The presence of subendometrial linear striations was the most specific sonographic feature (95.5%) and it had the highest PPV (80.0%) for the diagnosis of adenomyosis.

Conclusions

The presence of subendometrial echogenic linear striations, a globular configuration and myometrial cysts on transvaginal ultrasound supports the diagnosis of adenomyosis. Among the transvaginal ultrasound diagnostic findings of adenomyosis, subendometrial linear striations have the highest diagnostic accuracy. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Individual resource allocation to vegetative growth and reproduction in subgenus Cyclobalanopsis (Quercus, Fagaceae) trees
Authors: Hirayama Daisuke , Nanami Satoshi , Itoh Akira , Yamakura Takuo
Published: July 2007

The resource allocation for vegetative growth and female reproduction in three tree species of subgenus Cyclobalanopsis (Quercus, Fagaceae), i.e., Q. salicina, Q. sessilifolia, and Q. acuta, were examined on a per‐individual basis in two consecutive reproductive seasons, in order to test whether these trees fit the predictions of the masting hypotheses about resource matching versus resource switching. Since the three Quercus species have a biennial fruiting habit, it takes 3 years for the observation of two reproductive events. Female flower and acorn production per tree were investigated by using a seed‐trap method and a numerical analysis of seed dispersal. The net production of each individual was estimated as the sum of the annual increase in the dry mass of vegetative organs and reproductive investment per tree. In the data analyses, the three species were pooled, since all 12 sample trees of the subgenus apparently showed masting in the same year, with no exceptions. Female flower and acorn production per individual tree changed considerably between years. The net production per tree increased with tree size, but did not differ between years. Therefore, the reproductive allocation (proportion of a plant's annual assimilated resources which are used for reproduction) differed dramatically between years. On the other hand, within a year, the reproductive allocation increased with increasing net production per tree. These results suggest that the switching of resource allocation between years within an individual are occurring in subgenus Cyclobalanopsis species, and the intensity of the switching increases with increasing tree size.
Exclusive core areas and intrasexual territoriality in Eurasian red squirrels (Sciurus vulgaris) revealed by incremental cluster polygon analysis
Authors: Pierro Erica Di , Molinari Ambrogio , Tosi Guido , Wauters Lucas A.
Published: July 2007

When animal home ranges overlap extensively in species lacking overt territorial behaviours, identifying exclusive core areas within individual ranges can be difficult. By analysing the size and overlap of successively smaller core areas among individual Eurasian red squirrels (Sciurus vulgaris), we determined exclusive areas within the home ranges of resident males and females. Possible effects of habitat composition and food supplies were explored by monitoring squirrels in different conifer forests and during years with low and high tree seed production. Using outlier‐exclusive cores (OEC) revealed that the total ranges consisted of large sally zones (on average, 35% of the total minimum convex polygon [MCP] range) around home ranges with multi‐nucleate cores. The mean OEC home range size did not differ between the sexes but was larger with poor food availability. Home ranges (99% incremental cluster polygons [ICP]) overlapped extensively between sexes (average overlap high food–low food: males by females 21–40%, females by males 43–45%) and among males (males by males 26–44%), while intrasexual overlap among females was low (9–10%). The overlap of inner cores among females rapidly approached zero, suggesting the intrasexual territoriality of 75% core areas. This was not the case among male squirrels, for which intrasexual overlap averaged only 4% at 50% but 18% at 75% core areas. Even the smallest inner cores had some degree of intersexual overlap, indicating that complete territoriality did not occur in this species. Female home ranges were more strongly affected by annual fluctuations in food supplies than male ranges. Females reduced the size of their food‐based intrasexual territories when food availability increases. Males probably benefit from using larger home ranges and core areas, which overlap with the ranges of several females, by increasing their probability of successful mating.
Linoleic Acid Decreases Leptin and Adiponectin Secretion from Primary Rat Adipocytes in the Presence of Insulin
Authors: Pérez‐Matute P. , Martínez J. A. , Marti A. , Moreno‐Aliaga M. J.
Published: July 2007

Obesity rates have dramatically increased over the last few decades and, at the same time, major changes in the type of fatty acid intake have occurred. Linoleic acid, an n‐6 polyunsaturated fatty acid, is an essential fatty acid occurring in high amounts in several western diets. A potential role of this fatty acid on obesity has been suggested. Controversial effects of linoleic acid on insulin sensitivity have also been reported. Thus, the aim of this study was to examine the direct effects of linoleic acid on leptin and adiponectin production, two adipokines known to influence weight gain and insulin sensitivity. Because insulin‐stimulated glucose metabolism is an important regulator of leptin production, the effects of linoleic acid on adipocyte metabolism were also examined. For this purpose, isolated rat adipocytes were incubated with linoleic acid (1–200 μM) in the absence or presence of insulin. Linoleic acid (1–200 μM) significantly decreased insulin‐stimulated leptin secretion and expression (P< 0.05), however, no changes in basal leptin production were observed. Linoleic acid also induced a significant decrease (~20%) in adiponectin secretion (P< 0.05), but only in the presence of insulin and at the highest concentration tested (200 μM). This fatty acid did not modify either glucose uptake or lactate production and the percentage of glucose metabolized to lactate was not changed either. Together, these results suggest that linoleic acid seems to interfere with other insulin signalling pathway different from those controlling glucose uptake and metabolism, but involved in the regulation of leptin and adiponectin production.
Glycine receptor subunit composition alters the action of GABA antagonists
Authors: LI PING , SLAUGHTER MALCOLM
Published: July 2007

GABA receptor antagonists produce an unexpectedly significant inhibition of native glycine receptors in retina and in α1 or α2 homomeric glycine receptors (GlyRs) expressed in HEK 293 cells. In this study we evaluate this phenomenon in heteromeric glycine receptors, formed by mixing α1, α2, and β subunits. Picrotoxinin, picrotin, SR95531, and bicuculline are all more effective antagonists at GlyRs containing α2 subunits than α1 subunits. Inclusion of β subunits reduces the inhibitory potency of picrotoxinin and picrotin but increases the potency of SR95531 and bicuculline. As a result of these two factors, bicuculline is particularly poor at discriminating GABA and glycine receptors. Picrotin, which has been reported to be inactive at GABA receptors, blocks glycine currents in retina and in HEK293 cells, suggesting its utility as a selective glycine antagonist. However, picrotin is a more potent inhibitor of GABA than glycine in retinal neurons. We also tested if GABA and glycine receptor subunits can combine to form functional receptors. If GABAAR γ2S subunits are co-expressed with GlyR α subunits, the mixed receptor is glycine-sensitive and GABA-insensitive. But the mixed receptor exhibits a non-competitive picrotoxinin inhibition that is not observed in the homomeric GlyRs. This suggests that glycine and GABA subunits can co-assemble to form functional glycine receptors.
Modeling the movement of a pH perturbation and its impact on adsorbed zinc and phosphate in a wastewater‐contaminated aquifer
Authors: Kent D. B. , Wilkie J. A. , Davis J. A.
Published: July 2007

Chemical conditions were perturbed in an aquifer with an ambient pH of 5.9 and wastewater‐derived adsorbed zinc (Zn) and phosphate (P) contamination by injecting a pulse of amended groundwater. The injected groundwater had low concentrations of dissolved Zn and P, a pH value of 4.5 resulting from equilibration with carbon dioxide gas, and added potassium bromide (KBr). Downgradient of the injection, breakthrough of nonreactive Br and total dissolved carbonate concentrations in excess of ambient values (excess TCO2) were accompanied by a decrease in pH values and over twentyfold increases in dissolved Zn concentrations above preinjection values. Peak concentrations of Br and excess TCO2 were followed by slow increases in pH values accompanied by significant increases in dissolved P above preinjection concentrations. The injected tracers mobilized a significant mass of wastewater‐derived Zn. Reactive transport simulations incorporating surface complexation models for adsorption of Zn, P, hydrogen ions, and major cations onto the aquifer sediments, calibrated using laboratory experimental data, captured most of the important trends observed during the experiment. These include increases in Zn concentrations in response to the pH perturbation, perturbations in major cation concentrations, attenuation of the pH perturbation with transport distance, and increases in alkalinity with transport distance. Observed desorption of P in response to chemical perturbations was not predicted, possibly because of a disparity between the range of chemical conditions in the calibration data set and those encountered during the field experiment. Zinc and P desorbed rapidly in response to changing chemical conditions despite decades of contact with the sediments. Surface complexation models with relatively few parameters in the form of logK values and site concentrations show considerable promise for describing the influence of variable chemistry on the transport of adsorbing contaminants.
Modeling the 26 December 2004 Indian Ocean tsunami: Case study of impact in Thailand
Authors: Ioualalen M. , Asavanant J. , Kaewbanjak N. , Grilli S. T. , Kirby J. T. , Watts P.
Published: July 2007

The devastating 26 December 2004 Indian Ocean tsunami stressed the need for assessing tsunami hazard in vulnerable coastal areas. Numerical modeling is but one important tool for understanding past tsunami events and simulating future ones. Here we present a robust simulation of the event, which explains the large runups and destruction observed in coastal Thailand and identifies areas vulnerable to future tsunamis, or safer for reconstruction. To do so, we use an accurate tsunami source, which was iteratively calibrated in earlier work to explain the large‐scale tsunami features, and apply it over a computational domain with a finer grid and more accurate coastal bathymetry in Thailand. Computations are performed with a well‐validated numerical model based on fully nonlinear and dispersive Boussinesq equations (FUNWAVE) that adequately models the physics of tsunami propagation and runup, including dissipation caused by bottom friction and wave breaking. Simulated runups in Thailand reproduce field observations with a surprising degree of accuracy, as well as their high degree of along‐coast variation: a 92% correlation is found between (58) runup observations and computations, while the model explains 85% of the observed variance; overall, the RMS error is approximately 1 m or 17% of the mean observed runup value (skill of the simulation). Because we did not use runup observations to calibrate our coseismic tsunami source, these results are robust, and thus provide a uniquely accurate synoptic prediction of tsunami impact along the Andaman coast of Thailand, including those areas where no observations were made.
A long‐term regional simulation and observations of the hydroclimate in China
Authors: Qian Yun , Leung L. Ruby
Published: July 2007

This paper provides detailed analyses of observations and a 20‐year regional climate simulation to improve our understanding of the diverse hydroclimate regimes in China and examine model skill in simulating the seasonal, intraseasonal, and interannual hydroclimatic variations. Eastern China is greatly influenced by the East Asian monsoon, leading to heavy summer rainfall that exhibits large variations at the intraseasonal and interannual timescales. The Hai River and Huai River basins feature the largest interannual variations in summer rainfall followed by the middle and lower Yangtze River and Pearl River basins. In the wettest regions of the middle and lower Yangtze River basin (YRB) and Southeast Coast, the land surface plays a relatively passive role as evaporation is not limited by soil moisture. In the semiarid northern and western China, the land surface plays a more active role in the water cycle. This is supported by the strong correlations between soil moisture and sensible heat flux, evaporative fraction, and mixed‐layer depth, indicating a strong influence of soil wetness on atmospheric stability and precipitation processes. The overall spatial distribution, seasonal variations, and extreme precipitation are well simulated by the regional climate model (RCM). The model also captured the large‐scale spatial variations of annual mean soil moisture and runoff. However, the simulation produces more rainfall associated with the lower rain rates in central and southern China. Errors in the rain‐rate distributions can affect the simulation of surface hydrological processes. In addition, compared with the global reanalysis that provides the large‐scale boundary conditions, the simulation yielded lower anomaly correlations of interannual summer rainfall with observations. This suggests that simulating the interannual variability of rainfall at the river‐basin scale during the East Asian summer monsoon remains a significant challenge and deserves further studies to understand the causes for the model errors.
Effects of aerosols and relative humidity on cumulus clouds
Authors: Fan Jiwen , Zhang Renyi , Li Guohui , Tao Wei‐Kuo
Published: July 2007

The influences of the aerosol type and concentration and relative humidity (RH) on cumulus clouds have been investigated using a two‐dimensional spectral‐bin cloud model. Three simulations are conducted to represent the polluted continental, clean continental, and marine aerosol types. Under the same initial dynamic and thermodynamic conditions, the maritime aerosol case results in more intensive radar reflectivity in both developing and mature stages than the continental aerosol cases, because of enhanced warm rain by collisions and ice processes by deposition growth due to larger droplet sizes and higher supersaturation, respectively. The considerable delay in convective development due to reduced droplet condensation is responsible for the longer cloud lifetime in the marine aerosol case. For the continental case, the most noticeable effects of increasing aerosol number concentrations (with 15 different initial values) are the increases of the cloud droplet number concentration and cloud water content but a decrease in the effective droplet radius. More latent heat release from increasing condensation results in stronger convection and more melting precipitation at the higher aerosol concentrations. Melting precipitation and secondary clouds primarily contribute to enhanced precipitation with increasing aerosols. The precipitation, however, decreases with increasing aerosol in the extremely high aerosol cases (over 5 × 104 cm−3) due to suppression of convection from depleted water vapor and inefficient coalescence. When the initial aerosol concentration exceeds a critical level, most of the cloud properties become less sensitive to aerosols, implying that the aerosol effect on deep convection is more pronounced in relatively clean air than in heavily polluted air. The aerosol effect on the cloud properties is strongly dependent on RH. As the surface RH increases from 40 to 70%, the cloud changes from shallow warm to deep convective types due to a significant increase of convective available potential energy (CAPE). The aerosol effects on the cloud microphysical properties and precipitation are negligible in dry air (40% surface RH), but much more significant in humid air (60‐70% surface RH). The rain delay is sensitive to RH, but not to aerosols under similar initial thermodynamic conditions.
Stochastic finite element method for analysis of transport of nonlinearly sorbing solutes in three‐dimensional heterogeneous porous media
Authors: Chaudhuri A. , Sekhar M.
Published: July 2007

The probabilistic analysis by Monte Carlo simulation method (MCSM) for the transport of nonlinear reactive solutes in a three‐dimensional heterogeneous porous medium is a computationally prohibitive task. For linear transport problems, the perturbation‐based stochastic finite element method (SFEM) has been found to be computationally efficient with acceptable accuracy. This provides a motivation to develop the SFEM for the nonlinear reactive solute transport. In the present study, SFEM is developed for the transport of equilibrium nonlinear sorbing solutes, which follow the Langmuir‐Freundlich isotherm. This method produces a second‐order accurate mean and a first‐order accurate standard deviation of concentration. In this study, the governing medium propertis viz. hydraulic conductivity, dispersivity, molecular diffusion, porosity, sorption, and decay coefficients are considered to vary randomly in space. The performance of SFEM is compared to MCSM for both one‐ and three‐dimensional transport problems. The mean and the standard deviation of concentration for various test cases obtained with the SFEM compares well for the mild heterogeneity cases (standard deviation of log hydraulic conductivity less than 0.85) tested. SFEM produces a sharp front for the mean and the standard deviation of concentration while fronts obtained by MCSM are found to be dispersive. The error associated with the results obtained by SFEM is sensitive to the boundary conditions, the size of the domain, and the plume size. For a higher nonlinearity of sorption isotherm, the prediction uncertainty is higher. The pattern of the statistical moments of concentration is similar for cases with different correlation lengths of the parameters.
Flood frequency analysis at ungauged sites using artificial neural networks in canonical correlation analysis physiographic space
Authors: Shu C. , Ouarda T. B. M. J.
Published: July 2007

Models based on canonical correlation analysis (CCA) and artificial neural networks (ANNs) are developed to obtain improved flood quantile estimates at ungauged sites. CCA is used to form a canonical physiographic space using the site characteristics from gauged sites. Then ANN models are applied to identify the functional relationships between flood quantiles and the physiographic variables in the CCA space. Two ANN models, the single ANN model and the ensemble ANN model, are developed. The proposed approaches are applied to 151 catchments in the province of Quebec, Canada. Two evaluation procedures, the jackknife validation procedure and the split sample validation procedure, are used to evaluate the performance of the proposed models. Results of the proposed models are compared with the original CCA model, the canonical kriging model, and the original ANN models. The results indicate that the CCA‐based ANN models provide superior estimation than the original ANN models. The ANN ensemble approaches provide better generalization ability than the single ANN models. The CCA‐based ensemble ANN model has the best performance among all models in terms of prediction accuracy.
A correlated fracture network: Modeling and percolation properties
Authors: Masihi Mohsen , King Peter R.
Published: July 2007

We present a model of fractures based on the idea that the elastic free energy due to the fracture density follows a Boltzmann distribution. The resulting expression for the spatial correlation in the displacement of fractures is used as an objective function in a simulated annealing algorithm to generate realizations of correlated fracture networks. This approach determines the appropriate statistical distribution for the fractures (e.g., length distribution) rather than imposing them as is done conventionally. The model consists of two families of parallel fractures which are perpendicular under isotropic conditions. There also exists a positive correlation between the position of fractures and their lengths; that is, large fractures have their neighbors located at greater distance than small fractures. Finally, we use the realizations of correlated fracture networks in the basic methodology of the percolation approach and investigate the model percolation properties. In particular, the scaling exponents of the connectivity are found to be different from the conventional, uncorrelated values.
Extreme dynamic weakening of faults during dehydration by coseismic shear heating
Authors: Hirose Takehiro , Bystricky Misha
Published: July 2007

The dynamic strength of seismogenic faults has a critical effect on earthquake slip instability and seismic energy release. High velocity friction experiments on simulated faults in serpentinite at earthquake slip conditions show a decrease in friction coefficient from 0.6 to 0.15 as the slip velocity reaches 1.1 m/s at normal stresses up to 24.5 MPa. The extraordinary reduction in fault strength is attributed to flash heating at asperity contacts of gouge particles formed during sliding. The rapid heating at asperities causes serpentine dehydration. In impermeable fault zones in nature, serpentine dehydration and subsequent fluid pressurization due to coseismic frictional heating may promote further weakening. This dynamic fault‐weakening mechanism may explain the lack of pronounced heat flow in major crustal faults such as the San Andreas.
Local versus non‐local atmospheric weather noise and the North Pacific SST variability
Authors: Yeh Sang‐Wook , Kirtman Ben P. , An Soon‐Il
Published: July 2007

The interactive ensemble coupling strategy has been developed specifically to determine how noise impacts climate variability within context of coupled general circulation model (CGCM). This study examines the impacts of local versus non‐local noise on the North Pacific sea surface temperature anomaly (SSTA) variability using three CGCM simulations. The control run uses the standard coupling strategy. In the first experiment, the interactive ensemble strategy is applied globally thereby reducing the noise at the air‐sea interface at each grid point. In the second experiment, the interactive ensemble strategy is applied locally in the extra‐tropics only. Perhaps as expected, our analysis indicates that the impact of local noise on the North Pacific SSTA variability is much larger than that of non‐local noise. However, non‐local noise can not be neglected; for example, non‐local noise influences decadal SSTA variability in the central North Pacific. The hypothesis put forward here is that the noise due to enhanced tropical internal atmospheric variability causes the modulation of El Niño and Southern Oscillation, which in turn affects the North Pacific SSTA variability through the atmospheric bridge.
Emission of nonlinear whistler waves at the front of perpendicular supercritical shocks: Hybrid versus full particle simulations
Authors: Hellinger Petr , Trávníček Pavel , Lembège Bertrand , Savoini Philippe
Published: July 2007

New behavior of strictly perpendicular shocks in supercritical regime is analyzed with the help of both two‐dimensional (2‐D) hybrid and full particle electromagnetic simulations. Surprisingly, in both simulation cases, the shock front region appears to be dominated by emission of coherent large amplitude whistler waves for some plasma conditions and shock regimes. These whistler waves are oblique with respect to the shock normal as well as to the upstream magnetic field and are phase‐standing in the shock rest frame. A parametric study shows that these whistler waves are emitted in 2‐D perpendicular shocks and, simultaneously, the self‐reformation of the shock front associated with reflected ions disappears; the 2‐D shock front is almost quasi‐stationary. In contrast, both corresponding one‐dimensional (1‐D) hybrid and full particle simulations performed in similar plasma and Mach regime conditions show that the self‐reformation takes place for 1‐D perpendicular shock. These results indicate that the emission of these 2‐D whistler waves can inhibit the self‐reformation in 2‐D shocks. Possible generating mechanisms of these waves emissions and comparison with previous works are discussed.
Influence of β2‐adrenoceptor gene polymorphisms on β2‐adrenoceptor‐mediated responses in human lung mast cells
Authors: Kay L J , Rostami‐Hodjegan A , Suvarna S K , Peachell P T
Published: July 2007

Background and purpose:

Previous studies have shown that β
2‐adrenoceptor‐mediated responses in human lung mast cells are highly variable. The aims of the present study were to establish whether polymorphisms of the β
2‐adrenoceptor gene (ADRB2) influence this variability in (a) β
2‐adrenoceptor‐mediated inhibition and (b) desensitization of β
2‐adrenoceptor‐mediated responses in human lung mast cells.

Experimental approach:

Mast cells were isolated from human lung tissue. The inhibitory effects of the β‐adrenoceptor agonist, isoprenaline (10−10–10−5 M), on IgE‐mediated histamine release from mast cells were determined (n=92). Moreover, the inhibitory effects of isoprenaline were evaluated following a desensitizing treatment involving long‐term (24 h) incubation of mast cells with isoprenaline (10−6 M) (n=65). A potential influence of polymorphisms on these functional responses was determined by genotyping 11 positions, in the promoter and coding regions, of ADRB2 previously reported as polymorphic.

Key results:

There was no influence of any of the polymorphic positions of ADRB2 on the potency of isoprenaline to inhibit histamine release from mast cells with the exception of position 491C>T (Thr164Ile). There was no influence of any of the polymorphic positions of ADRB2 on the extent of desensitization of the isoprenaline‐mediated response following a desensitizing treatment except for position 46G>A (Gly16Arg). Analyses at the haplotype level indicated that there was no influence of haplotype on β
2‐adrenoceptor‐mediated responses in mast cells.

Conclusions and implications:

These data indicate that certain polymorphisms in ADRB2 influence β
2‐adrenoceptor‐mediated responses in human lung mast cells.

British Journal of Pharmacology (2007) 152, 323–331; doi:10.1038/sj.bjp.0707400; published online 23 July 2007
Evaluation and eligibility of HLA‐identical sibling donors for stem cell/bone marrow donation
Authors: Morrison A. E. , Green R. H. A. , Watson D. M. , Franklin I. M.
Published: July 2007

Overall, the number of allogeneic transplants performed world‐wide has not increased dramatically over the past 5 years. However, the proportion of allogeneic transplants undertaken using peripheral blood progenitor cells (PBPCs) has risen significantly. Currently, as part of an ethically approved trial, potential donors are seen, assessed and consented by physicians not caring directly for the recipients. Thirty‐five potential sibling donors were seen and assessed for their willingness and fitness to donate for 28 patients. One donor opted to give bone marrow and the rest selected PBPC donation. Seven of these donors were found to have concurrent medical conditions. Due to poor venous access, one donor was advised to donate bone marrow and two others donated bone marrow due to an underlying condition. Four others were deemed unfit for donation. Donation of stem cells from bone marrow or peripheral blood is not a risk‐free procedure; careful preassessment and counselling is mandatory especially when the age of prospective patients and therefore donors is increasing.