bluuebunny/crossref_metadata_2025 huggingface dataset:
Depth‐integrated, non‐hydrostatic model with grid nesting for tsunami generation, propagation, and run‐up
Authors: Yamazaki Yoshiki , Cheung Kwok Fai , Kowalik Zygmunt
Published: December 2010

Tsunamis generated by earthquakes involve physical processes of different temporal and spatial scales that extend across the ocean to the shore. This paper presents a shock‐capturing dispersive wave model in the spherical coordinate system for basin‐wide evolution and coastal run‐up of tsunamis and discusses the implementation of a two‐way grid‐nesting scheme to describe the wave dynamics at resolution compatible to the physical processes. The depth‐integrated model describes dispersive waves through the non‐hydrostatic pressure and vertical velocity, which also account for tsunami generation from dynamic seafloor deformation. The semi‐implicit, finite difference model captures flow discontinuities associated with bores or hydraulic jumps through the momentum‐conserved advection scheme with an upwind flux approximation. The two‐way grid‐nesting scheme utilizes the Dirichlet condition of the non‐hydrostatic pressure and both the horizontal velocity and surface elevation at the inter‐grid boundary to ensure propagation of dispersive waves and discontinuities across computational grids of different resolution. The inter‐grid boundary can adapt to bathymetric features to model nearshore wave transformation processes at optimal resolution and computational efficiency. A coordinate transformation enables application of the model to small geographic regions or laboratory experiments with a Cartesian grid. A depth‐dependent Gaussian function smoothes localized bottom features in relation to the water depth while retaining the bathymetry important for modeling of tsunami transformation and run‐up. Numerical experiments of solitary wave propagation and N‐wave run‐up verify the implementation of the grid‐nesting scheme. The 2009 Samoa Tsunami provides a case study to confirm the validity and effectiveness of the modeling approach for tsunami research and impact assessment. Copyright © 2010 John Wiley & Sons, Ltd.
A Numerical Study of Structural Change and Anisotropic Permeability in Compressed Carbon Cloth Polymer Electrolyte Fuel Cell Gas Diffusion Layers
Authors: Rama P. , Liu Y. , Chen R. , Ostadi H. , Jiang K. , Gao Y. , Zhang X. , Brivio D. , Grassini P.
Published: December 2010

The effect of compression on the actual structure and transport properties of the carbon cloth gas diffusion layer (GDL) of a polymer electrolyte fuel cell (PEFC) are studied here. Structural features of GDL samples compressed in the 0.0–100.0 MPa range are encapsulated using polydimethylsiloxane (PDMS) and by employing X‐ray micro‐tomography to reconstruct direct digital 3D models. Pore size distribution (PSD) and porosity data are acquired directly from these models while permeability, degree of anisotropy and tortuosity are determined through lattice Boltzmann (LB) numerical modelling. The structural models reveal that structural change proceeds through a three‐step process, while PSD data suggests a characteristic peak in the pore diameter of 10–14 μm and a decrease in the mean pore diameter from 33 to 12 μm over the range of tested pressures. A mathematical relationship between compression pressure and permeability is determined based on the Kozeny–Carman equation, revealing a one order of magnitude reduction in through‐plane permeability for a two order of magnitude increase in pressure. The results also reveal that the degree of anisotropy peaks in the range of 0.3–10.0 MPa, suggesting that in‐plane permeability can be maximised relative to through‐plane permeability within a material‐specific range of compression pressures.
Organizational analysis of maternal mortality reduction programs in Madagascar
Authors: Harimanana Aina , Barennes Hubert , Reinharz Daniel
Published: December 2010

Little is known about the organizational factors involved in policy creation and programs implementation aimed at reducing maternal mortality in Madagascar. A qualitative case study was performed to investigate organizational factors influencing the health system's capacity to elaborate and implement maternal mortality reduction programs. Semi‐structured interviews were conducted with 53 participants. A conceptual framework based on Gamson's coalition theory and Hinings and Greenwood's archetypes concept was used. Three major conclusions emerge: the Ministry of Health is a poor leader in the development of national strategies, due to its dependency on external financial resources and expertise, and because of poor transmission of key information from the field; at a meso level (regions and districts), the capacity to adapt programs is highly dependent on the collaboration with NGOs; at the micro level, there are few incentives provided to field workers to participate in a collective effort and little attempt to exploit complementarities between scare resources. The Madagascar health system should consider the need for improvement in data analysis capacity, and implementing behavior‐changing tools suitable for stimulating providers who work inside and outside the health care system, to participate to a coordinated collective effort. Copyright © 2010 John Wiley & Sons, Ltd.
Xylitol inhibits carcinogenic acetaldehyde production by Candida species
Authors: Uittamo Johanna , Nieminen Mikko T. , Kaihovaara Pertti , Bowyer Paul , Salaspuro Mikko , Rautemaa Riina
Published: December 2010

Acetaldehyde is a highly toxic and mutagenic product of alcohol fermentation and metabolism which has been classified as a Class I carcinogen for humans by the International Agency for Research on Cancer of the World Health Organisation (WHO). Many Candida species representing oral microbiota have been shown to be capable of marked acetaldehyde production. The aim of our study was to examine the effects of various sugar alcohols and sugars on microbial acetaldehyde production. The study hypothesis was that xylitol could reduce the amount of acetaldehyde produced by Candida. Laboratory and clinical isolates of seven Candida species were selected for the study. The isolates were incubated in 12 mM ethanol and 110 mM glucose, fructose or xylitol at 37°C for 30 min and the formed acetaldehyde was measured by gas chromatography. Xylitol significantly (p < 0.0001) reduced the amount of acetaldehyde produced from ethanol by 84%. In the absence of xylitol, the mean acetaldehyde production in ethanol incubation was 220.5 μM and in ethanol–xylitol incubation 32.8 μM. This was found to be mediated by inhibition of the alcohol dehydrogenase enzyme activity. Coincubation with glucose reduced the amount of produced acetaldehyde by 23% and coincubation with fructose by 29%. At concentrations that are representative of those found in the oral cavity during the intake of proprietary xylitol products, xylitol was found to reduce the production of carcinogenic acetaldehyde from ethanol by Candida below the mutagenic level of 40–100 μM.
Fluoride‐induced genotoxicity in mouse bone marrow cells: effect of buthionine sulfoximine andN‐acetyl‐l‐cysteine
Authors: Podder Santosh , Chattopadhyay Ansuman , Bhattacharya Shelley , Ray Manas Ranjan , Chakraborty Anindita
Published: December 2010

A significant level of reactive oxygen species generation was observed in sodium fluoride (NaF) treated mouse bone marrow cells (BMCs). Reduced glutathione (GSH) as a free radical scavenger could be an important determining factor in F‐induced genotoxicity. We therefore attempted to monitor GSH to understand the mechanism of NaF‐induced genotoxicity. NaF was injected intra‐peritoneally in normal, buthionine sulfoximine (BSO) orN‐acetyl‐l‐cysteine (NAC) treated mice (n= 5). After 13 h of NaF‐treatment BMCs were collected to harvest them at the same divisional cycle and processed for analysis of cell cycle, induction of apoptosis and chromosomal aberrations (CAs). Level of GSH was also measured concomitantly. NaF induced significant CAs in all treatment groups except at 2.5 mg NaF kg−1body weight. BSO‐treatment alone induced significantly high frequency of CAs. BSO treatment prior to injection of 2.5–7.5 mg NaF kg−1b.w. was found to increase the frequency of CAs, significantly when compared with the positive control group, but the level was not significant in case of higher doses of NaF treatment (15 and 30 mg kg−1b.w.). NaF‐treated cells also showed a higher population of Annexin‐V positive cells. NAC pre‐treatment significantly reduced the extent of NaF‐induced CAs, which clearly indicates the involvement of GSH in the NaF response. However, further study is warranted to evaluate the low synergistic effect of BSO on higher doses of NaF‐induced CAs. Copyright © 2010 John Wiley & Sons, Ltd.
Decontamination of collagen biomatrices with combined pulsed electric field and nisin treatment
Authors: Griffiths Sarah , Maclean Michelle , MacGregor Scott J. , Anderson John G. , Helen Grant M.
Published: December 2010

Pulsed electric field (PEF) treatment has been proposed as a decontamination method for labile matrices used in tissue engineering applications. Through the application of PEF, a non‐thermal treatment that causes bacterial inactivation through the irreversible rupture of microbial cell membranes, inactivation is achieved without loss of scaffold structure and function. However, some microorganisms are less susceptible to PEF treatment. This study shows that treatment with PEF and nisin, a food preservative bacteriocin, has a synergistic effect on the inactivation of Staphylococcus epidermidis in collagen gels. Almost complete inactivation of a 103–104 CFU/mL S. epidermidis population was achieved when treated with a combination of PEF and 500 IU/mL nisin, with results demonstrating a 3.4 log10 reduction, compared with 0.66 log10 reduction with PEF alone. Nisin, at concentrations up to 3000 IU/mL, had no discernable toxicity to mammalian 3T3 cells when added to the culture medium or incorporated into the collagen gels. This combined decontamination method, involving PEF plus nisin, may provide a non‐destructive process for inactivation of PEF‐resistant bacteria in labile tissue engineering scaffolds. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
Comparison of antioxidant effectiveness of lipoic acid and dihydrolipoic acid
Authors: Zhao Feng , Liu Zai‐Qun
Published: December 2010

The abilities of dihydrolipoic acid (DHLA) to scavenge peroxynitrite (ONOO−), galvinoxyl radical, 2,2′‐azinobis(3‐ethylbenzothiazoline‐6‐sulfonate) cation radical (ABTS+•), and 2,2′‐diphenyl‐1‐picrylhydrazyl radical (DPPH) were higher than those of lipoic acid (LA). The effectiveness of DHLA to protect methyl linoleate against 2,2′‐azobis(2‐amidinopropane hydrochloride) (AAPH)‐induced oxidation was about 2.2‐fold higher than that of LA, and DHLA can retard the autoxidation of linoleic acid (LH) in the β‐carotene‐bleaching test. DHLA can also trap ∼0.6 radicals in AAPH‐induced oxidation of LH. Moreover, DHLA can scavenge ∼2.0 radicals in AAPH‐induced oxidation of DNA and AAPH‐induced hemolysis of erythrocytes, whereas LA can scavenge ∼1.5 radicals at the same experimental conditions. DHLA can protect erythrocytes against hemin‐induced hemolysis, but accelerate the degradation of DNA in the presence of Cu2+. Therefore, the antioxidant capacity of –SH in DHLA is higher than S‐S in LA. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 25:216–223, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/jbt.20378
Effect of tin and lead chlorotriphenyl analogues on selected living cells
Authors: Boniewska‐Bernacka Ewa , Man Dariusz , Słota Rudolf , Broda Małgorzata A.
Published: December 2010

Three kinds of living cells, human embryonic kidney cells, Saccharomyces cerevisiae, and Escherichia coli, were tested for their sensitivity to chlorotriphenyltin and chlorotriphenyllead. The tin compound proved definitely more toxic than the lead derivative, particularly in the case of the human embryonic kidney cells devoid of any protective cell wall. Electron paramagnetic resonance (EPR) comparative studies carried out by using a natural model liposome system (egg yolk lecithin) confirmed considerable changes within the lipid bilayer upon doping by the aforementioned additives, which may be crucial to the mechanism of the observed cell cleavage. The individual dopants revealed diverse impact upon the membrane's condition, chlorotriphenyltin distinctly fluidized the lipid system, whereas chlorotriphenyllead stiffened the medium within the membrane. A theoretical approach concerning such different behaviors of studied tin and lead analogues because of their high toxicity in living cells has been presented. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 25:231–237, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/jbt.20380
Visualization of intracellular trafficking of Math1 protein in different cell types with a newly‐constructed nonviral gene delivery plasmid
Authors: Zhang Weikai , Zhang Ya , Sood Rohit , Ranjan Sanjeev , Surovtseva Elena , Ahmad Aqeel , Kinnunen Paavo K. J. , Pyykkö Ilmari , Zou Jing
Published: December 2010

Background

In recent years, Math1 gene therapy was indicated to be the future therapy for deafness in combination with other growth factors. However, Math1 delivery using adenovirus‐mediated gene delivery or electroporation was impractical. The contribution of Math1 in the combined procedure was not clearly elucidated using the existing plasmids. Nonviral gene delivery vectors are expected to be extremely safe and convenient. The present study aimed to construct the pCDNA6.2/C‐EmGFP‐Math1 plasmid and evaluate its transfection efficiency and intracellular trafficking of Math1 protein corresponding to transcription regulation function.

Methods

After constructing the pCDNA6.2/C‐EmGFP‐Math1 expression plasmid, the plasmid was transfected into different cell lines and primary cochlear cells using Lipofectamine 2000. Transfection efficiencies of the plasmid were evaluated. Transfection efficiencies using liposome nanoparticles containing Math1 plasmid were also assessed. Intracellular trafficking of Math1 was monitored using confocal microscopy.

Results

Different cell types can be transfected with high transfection efficiencies by the pcDNA6.2/C‐EmGFP‐Math1 plasmid using Lipofectamine 2000. Liposome nanoparticles containing the Math1 plasmid expressed the gene with variable efficiencies, depending on the particle size, surface charge and PEGylation status. Unique intracellular trafficking of Math1 was demonstrated in different cell types.

Conclusions

The newly‐constructed plasmid pcDNA6.2/C‐EmGFP‐Math1 was suitable for nonviral gene delivery of Math1. Unique intracellular trafficking of Math1 with dynamics from the cytoplasm to the nucleus was demonstrated. The modification of mesenchymal stem cells by Math1 gene delivery and by brain‐derived neurotrophic factor and glial cell line‐derived neurotrophic factor treatments can potentially be applied to cell replacement for the treatment of cochlear spiral ganglion cell loss in deafness. Copyright © 2011 John Wiley & Sons, Ltd.
Synthesis and antioxidant activity of novel 15‐alkyl/aryl‐13, 17‐dihydro‐15λ5‐dibenzo [e, k] [1, 3, 7, 10, 2] dioxadiazaphosphacyclotridecin‐15‐selones/thiones/ones
Authors: Naidu K. Reddi Mohan , Kumar M. Anil , Dadapeer E. , Babu K. Ramesh , Raju C. Naga , Ghosh S. K.
Published: December 2010

A new class of phosphorus macrocycles were synthesized from 2‐[(E)‐2‐2 [(hydroxymethyl) phenyl] imino ethylidene) amino] phenyl methanol 1 with various phenylphosphorodichloridates, phenyldichlorophosphine, and ethyldichlorophosphite in the presence of triethylamine at 0–10°C under N2 atmosphere in THF. All the title compounds were confirmed by analytical and spectral data (IR, 1H‐, 13C‐, 31P‐NMR, and mass). The title compounds exhibited promising anti‐oxidant activity. J. Heterocyclic Chem., (2011).
A novel route to 4‐oxy/thio substituted‐1H‐pyrazol‐5(4H)‐ones via efficient cross‐Claisen condensation
Authors: Ragavan R. Venkat , Vijayakumar V.
Published: December 2010

α‐Oxy/thio substituted β‐keto esters were synthesized through an efficient cross‐Claisen condensation of oxy/thio substituted acetic acid ethyl esters with acid chlorides, which in turn converted in situ into 4‐oxy/thio substituted‐1H‐pyrazol‐5(4H)‐ones by the addition of hydrazine and its derivatives. This method has been found to be extremely fast, general, and useful toward the synthesis of inaccessible pyrazolones and synthetically demanding 4‐oxy/thio substituted pyrazolones. J. Heterocyclic Chem., (2011).
Childhood traumatic stress and obesity in women: The intervening effects of PTSD and MDD
Authors: Dedert Eric A. , Becker Mary E. , Fuemmeler Bernard F. , Braxton Loretta E. , Calhoun Patrick S. , Beckham Jean C.
Published: December 2010

In this study, symptoms of posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) were modeled as intervening variables in the relationship between childhood traumatic stress and weight outcomes in civilian women in the United States. Of the 148 participants, 72 had current PTSD, 64 had current MDD, and 32 had neither disorder. In separate single indirect effect models, there were significant indirect effects of both PTSD and depressive symptoms on body mass index and waist–hip ratio. When models included both PTSD and depressive symptoms, an indirect effect of PTSD symptoms was evident in the relationship between childhood traumatic stress and waist–hip ratio. Posttraumatic stress disorder may play a particularly important role in the development of central adiposity.
A polymorphism at –1607 2G in the matrix metalloproteinase‐1 (MMP‐1) increased risk of sudden deafness in korean population but not at –519A/G in MMP‐1
Authors: Nam Sung‐Il , Yu Gyeong‐Im , Kim Hak‐Jae , Park Kyoung‐Ok , Chung Joo‐Ho , Ha Eunyoung , Shin Dong‐Hoon
Published: December 2010

Objectives/Hypothesis:

Matrix metalloproteinase‐1 (MMP‐1) is associated with a risk of inflammatory disease and cancer invasion. Two common etiologies for sudden deafness (SD) are circulatory disturbance and inflammation. The present study aimed to investigate whether MMP‐1 polymorphisms are associated with SD.

Study Design:

Case‐control study. Ninety‐nine Korean SD patients and 530 normal patients (controls) were used in this study.

Methods:

Single nucleotide polymorphism (SNP) of MMP‐1 (at –1607G/2G and –519A/G) was analyzed using the pyrosequencing method.

Results:

At MMP‐1 –1607G/2G, the distributions of 2G/2G, G/2G, and G/G genotypes in controls were 36.8%, 44.3%, and 18.9%, respectively, and in SD patients were 46.5%, 48.5%, and 5.1%, respectively. The 2G/2G genotype was found to increase the risk of SD compared with the G/G genotype (codominant model: P = .0029; recessive model: P = .0003). The 2G allele was found to increase the risk of SD compared with the G allele (P = .002). At MMP1 –519A/G, there was no statistically significant increase in the risk of SD. Among haplotypes of MMP‐1 polymorphisms –1607G/2G and –519A/G, 2GA and GA were found to be associated with SD (P < .05).

Conclusions:

These results suggest that the 2G/2G genotype is associated with an increased risk of SD compared with the G/2G and G/G genotypes. Furthermore, the 2G allele may be a risk factor for SD. Laryngoscope, 2011
Heat‐induced Supramolecular Crosslinking of Dumbbell‐shaped PEG with β‐CD Dimer Based on Reversible Loose‐fit Rotaxanation
Authors: Katoono Ryo , Kobayashi Yuichiro , Yamaguchi Masayuki , Yui Nobuhiko
Published: December 2010

Supramolecular crosslinking was studied in reversible loose‐fit rotaxanation between a size‐mismatched ring and a dumbbell‐shaped chain attached to bulky terminals through slipping of the crosslinked rings onto the chain using a combination of β‐cyclodextrin (β‐CD) and poly(ethylene glycol) (PEG) in water. The mixing led to a drastic increase in viscosity only at an elevated temperature, while a PEG chain without any terminals or with bulkier terminals produced no change in the mixed solution under the same conditions. The dynamic viscoelastic properties of the mixed solution of the proper dumbbell‐shaped PEG chain and β‐CD dimer in water were also investigated to indicate network formation through heat‐induced supramolecular crosslinking.

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Quality index scheme for quantitative uncertainty characterization of radar‐based precipitation
Authors: Szturc Jan , Ośródka Katarzyna , Jurczyk Anna
Published: December 2010

A quality index scheme is proposed which is designed to evaluate the quality of different radar‐derived rainfall products including processed radar data and precipitation accumulations. The idea of the quality index scheme is based on selection of quality factors, determination of their quality indices and computation of one final quality index. The factors were selected depending on the particular kind of precipitation field. In the proposed scheme the quality index for each quality factor is determined using regression relationships between quality factors and data errors calculated from rain gauge—radar observation differences. Finally, all the individual quality indices are summarized to a final quality index applying appropriate weights. The quality index is computed for each pixel of radar‐derived precipitation field independently. The quality information field obtained in this way is attached to the radar‐based precipitation product and can be used to generate the precipitation field as percentiles of probability density functions. Copyright © 2010 Royal Meteorological Society
Performance evaluation of evapotranspiration estimations in a model of soil water balance
Authors: Gassmann María , Gardiol Jesús , Serio Leonardo
Published: December 2010

Soil water content models have huge applications from an agronomic point of view and they are usually used as a sub‐model for weather and climate modelling. They are also useful tools for efficient water management irrigation practices. The aim of this investigation is to evaluate the performance of two different parameterizations of evapotranspiration when applied to a soil water balance model. Experimental data of a maize crop is used to evaluate model accuracy. The first methodology proposes a parallel resistance arrangement to represent the latent heat fluxes of the soil surface and the leaves in the canopy layer considering the leaf area index (LAI). The second methodology uses the parameterization proposed by the United Nations Food and Agriculture Organization (FAO), based on the crop coefficient (Kc) and the potential evapotranspiration obtained from the Penman–Monteith equation. The crop was divided into five plots with different irrigation systems according to their phenological stages. The model suitably predicts daily soil water content in five different irrigation systems. Predictions of soil water content using the LAI or Kc methodology tend to overestimate observations. In addition, the model has better predictions using the LAI methodology than the Kc methodology. The root mean square error and the determination coefficient were 0.059 and 0.92, respectively, with the LAI methodology and 0.063 and 0.87, respectively, using the Kc methodology. Copyright © 2010 Royal Meteorological Society
cables1 is required for embryonic neural development: molecular, cellular, and behavioral evidence from the zebrafish
Authors: Groeneweg Jolijn W. , White Yvonne A.R. , Kokel David , Peterson Randall T. , Zukerberg Lawrence R. , Berin Inna , Rueda Bo R. , Wood Antony W.
Published: December 2010

In vitro studies have suggested that the Cables1 gene regulates epithelial cell proliferation, whereas other studies suggest a role in promoting neural differentiation. In efforts to clarify the functions of Cables1 in vivo, we conducted gain‐ and loss‐of‐function studies targeting its ortholog (cables1) in the zebrafish embryo. Similar to rodents, zebrafish cables1 mRNA expression is detected most robustly in embryonic neural tissues. Antisense knockdown of cables1 leads to increased numbers of apoptotic cells, particularly in brain tissue, in addition to a distinct behavioral phenotype, characterized by hyperactivity in response to stimulation. Apoptosis and the behavioral abnormality could be rescued by co‐expression of a morpholino‐resistant cables1 construct. Suppression of p53 expression in cables1 morphants partially rescued both apoptosis and the behavioral phenotype, suggesting that the phenotype of cables1 morphants is due in part to p53‐dependent apoptosis. Alterations in the expression patterns of several neural transcription factors were observed in cables1 morphants during early neurulation, suggesting that cables1 is required for early neural differentiation. Ectopic overexpression of cables1 strongly disrupted embryonic morphogenesis, while overexpression of a cables1 mutant lacking the C‐terminal cyclin box had little effect, suggesting functional importance of the cyclin box. Lastly, marked reductions in p35, but not Cdk5, were observed in cables1 morphants. Collectively, these data suggest that cables1 is important for neural differentiation during embryogenesis, in a mechanism that likely involves interactions with the Cdk5/p35 kinase pathway. Mol. Reprod. Dev. 78:22–32, 2011. © 2010 Wiley‐Liss, Inc.
Beyond pressure stabilization: A low‐order local projection method for the Oseen equation
Authors: Barrenechea Gabriel R. , Valentin Frédéric
Published: December 2010

This work proposes a new local projection stabilized finite element method (LPS) for the Oseen problem. The method adds to the Galerkin formulation new fluctuation terms that are symmetric and easily computable at the element level. Proposed for the pair ℙ1/ℙl, l = 0, 1, when the pressure is continuously or discontinuously approximated, well‐posedness and error optimality are proved. In addition, we introduce a cheap strategy to recover an element‐wise mass conservative velocity field in the discontinuous pressure case, a property usually neglected in the stabilized finite element context. Numerics validate the theoretical results and show that the present method improves accuracy to represent boundary layers when compared with alternative approaches. Copyright © 2010 John Wiley & Sons, Ltd.
Acceleration of DEM algorithm for quasistatic processes
Authors: Padbidri Jagan M. , Mesarovic Sinisa Dj.
Published: December 2010

The discrete element method (particle dynamics) is an invaluable tool for studying the complex behavior of granular matter. Its main shortcoming is its computational intensity, arising from the vast difference between the integration time scale and the observation time scale (similar to molecular dynamics). This problem is particularly acute for macroscopically quasistatic deformation processes. We first provide the proper definition of macroscopically quasistatic processes, on the basis of dimensional analysis, which reveals that the quasistatic nature of a process is size‐dependent. This result sets bounds for application of commonly used method for computational acceleration, based on superficially increased mass of particles. Next, the dimensional analysis of the governing equations motivates the separation of time scales for the numerical integration of rotations and translations. We take advantage of the existence of fast and slow variables (rotations and translations) to develop a two‐timescales algorithm based on the concept of inertial manifolds suggested by Gear and Kevrekidis. The algorithm is tested on a 2D problem with axial strain imposed by rigid plates and pressure on lateral boundaries. The benchmarking against the accurate short‐time step results confirms the accuracy of the new algorithm for the optimal arrangement of short‐ and long‐time steps. The algorithm provides moderate computational acceleration. Copyright © 2010 John Wiley & Sons, Ltd.
Adaptive component mode synthesis in linear elasticity
Authors: Jakobsson Håkan , Bengzon Fredrik , Larson Mats G.
Published: December 2010

Component mode synthesis (CMS) is a classical method for the reduction of large‐scale finite element models in linear elasticity. In this paper we develop a methodology for adaptive refinement of CMS models. The methodology is based on a posteriori error estimates that determine to what degree each CMS subspace influence the error in the reduced solution. We consider a static model problem and prove a posteriori error estimates for the error in a linear goal quantity as well as in the energy and L2 norms. Automatic control of the error in the reduced solution is accomplished through an adaptive algorithm that determines suitable dimensions of each CMS subspace. The results are demonstrated in numerical examples. Copyright © 2010 John Wiley & Sons, Ltd.
Access to international volunteering
Authors: McBride Amanda Moore , Lough Benjamin J.
Published: December 2010

Using the 2005 U.S. Current Population Survey, we identify the demographic profile of international volunteers from the United States. According to logistic regression results, those most likely to volunteer internationally are young, white, male, highly educated, foreign‐born individuals without dependent children in the home and not employed full time. These findings are discussed through the lens of access and inclusion, examining the possible influences of individual choice and programmatic structure on this demographic profile. Implications are drawn for future research.
Five dimensions of effectiveness for nonprofit annual reports
Authors: Gordon Teresa P. , Khumawala Saleha B. , Kraut Marla , Neely Daniel G.
Published: December 2010

Annual reports are an important communication device through which nonprofit entities can satisfy their duty to be accountable to donors and the public at large. The primary objective of this article is to identify best practices for annual reports based on five dimensions: completeness, accessibility, transparency, full disclosure, and relevance. This article reports on both the financial and nonfinancial content in voluntarily provided annual reports. Based on our survey, we include recommendations and examples to help nonprofit leaders improve communication with stakeholders. While many of the recommendations can be adopted at little or no additional cost, achieving the most important criterion, relevance, will require nonprofit leaders to substantially improve their reporting of organizational goals and accomplishments.
Thalassaemia: Its diagnosis and interpretation in past skeletal populations
Authors: Lewis M. E.
Published: December 2010

The diagnosis of thalassaemia in archaeological populations has long been hindered by a lack of pathogonomic features, and the non‐specific nature of cribra orbitalia and porotic hyperostosis. In fact, clinical research has highlighted more specific diagnostic criteria for thalassaemia major and intermedia based on changes to the thorax (‘rib‐within‐a‐rib’ and costal osteomas). A recent re‐examination of 364 child skeletons from Romano‐British Poundbury Camp, Dorset revealed children with general ‘wasting’ of the bones and three children who demonstrated a variety of severe lesions (e.g. zygomatic bone and rib hypertrophy, porotic hyperostosis, rib lesions, osteopenia and pitted diaphyseal shafts) that are inconsistent with dietary deficiency alone, and more consistent with a diagnosis of genetic anaemia. Two of these children displayed rib lesions typical of those seen in modern cases of thalassaemia. The children of Poundbury Camp represent the first cases of genetic anaemia identified in a British archaeological population. As thalassaemia is a condition strongly linked to Mediterranean communities, the presence of this condition in a child from England, found within a mausoleum, suggests that they were born to wealthy immigrant parents living in this small Roman settlement in Dorset. This paper explores the diagnostic criteria for genetic anaemia in the archaeological literature and what its presence in ancient populations can contribute to our knowledge of past human migration. Copyright © 2010 John Wiley & Sons, Ltd.
Characterisation of proteins extracted from the surface of Salmonella Typhimurium grown under SPI‐2‐inducing conditions by LC‐ESI/MS/MS sequencing
Authors: Sherry Aileen E. , Inglis Neil F. , Stevenson Andy , Fraser‐Pitt Douglas , Everest Paul , Smith David G. E. , Roberts Mark
Published: December 2010

Salmonella enterica has two pathogenicity islands encoding separate type three secretion systems (T3SS). Proteins secreted through these systems facilitate invasion and survival. After entry, Salmonella reside within a membrane bound vacuole, the Salmonella containing vacuole (SCV), where translocation of a second set of effectors by the Salmonella pathogenicity island 2 (SPI‐2) T3SS is initiated. SPI‐2 secretion in vitro can be induced by conditions that mimic the Salmonella containing vacuole. Utilising high‐throughput mass spectrometry, we mapped the surface‐attached proteome of S. Typhimurium SL1344 grown in vitro under SPI‐2‐inducing conditions and identified 108 proteins; using secretion signal prediction software, 43% of proteins identified contained a signal sequence. Of these proteins, 13 were known secreted effector proteins including SPI‐2 effector proteins SseB, SseC, SseD, SseL, PipB2 and SteC, although surprisingly five were SPI‐1 proteins, SipA, SipB, SipC, SipD and SopD, while 2 proteins SteA and SlrP are secreted by both T3SSs. This is the first in vitro study to demonstrate dual secretion of SPI‐1 and SPI‐2 proteins by S. Typhimurium and demonstrates the potential of high‐throughput LC‐ESI/MS/MS sequencing for the identification of novel proteins, providing a platform for subsequent comparative proteomic analysis, which should greatly assist understanding of the pathogenesis and inherent variation between serovars of Salmonella and ultimately help towards development of novel control strategies.
Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post‐translational modifications
Authors: Casado‐Vela Juan , Cebrián Arancha , Gómez del Pulgar Maria Teresa , Sánchez‐López Elsa , Vilaseca Marta , Menchén Laura , Diema Claudia , Sellés‐Marchart Susana , Martínez‐Esteso María José , Yubero Noemí , Bru‐Martínez Roque , Lacal Juan Caelos
Published: December 2010

Recent reviews pinpointed the enormous diversity of proteins found in living organisms, especially in higher eukaryotes. Protein diversity is driven through three main processes: first, at deoxyribonucleic acid (DNA) level (i.e. gene polymorphisms), second, at precursor messenger ribonucleic acid (pre‐mRNA) or messenger ribonucleic acid (mRNA) level (i.e. alternative splicing, also termed as differential splicing) and, finally, at the protein level (i.e. PTM). Current proteomic technologies allow the identification, characterization and quantitation of up to several thousands of proteins in a single experiment. Nevertheless, the identification and characterization of protein species using these technologies are still hampered. Here, we review the use of the terms “protein species” and “protein isoform.” We evidence that the appropriate selection of the database used for searches can impede or facilitate the identification of protein species. We also describe examples where protein identification search engines systematically fail in the attribution of protein species. We briefly review the characterization of protein species using proteomic technologies including gel‐based, gel‐free, bottom‐up and top‐down analysis and discuss their limitations. As an example, we discuss the theoretical characterization of the two human choline kinase species, α‐1 and α‐2, sharing the same catalytic activity but generated by alternative splicing on CHKA gene.
Recent advances in the use ofSus scrofa(pig) as a model system for proteomic studies
Authors: Verma Nisha , Rettenmeier Albert W. , Schmitz‐Spanke Simone
Published: December 2010

Of the numerous animal models available for proteomic studies only a small number have been successfully used in understanding human biology. To date, rodents have been widely employed in proteomic and genomic studies but often these models do not truly mimic the relevant human conditions. On the other hand, the pig shows similarity in size, shape and physiology to human and has been used as a major mammalian model for many studies concerning xenotransplantation, cardiovascular diseases, blood dynamics, nutrition, general metabolic functions, digestive‐related disorders, respiratory diseases, diabetes, kidney and bladder diseases, organ‐specific toxicity, dermatology and neurological sequelae. With the substantially improved knowledge of the structure and function of the pig genome in the last two decades it has been found that this animal shares a high sequence and chromosomal structure homology with humans. Nevertheless, in comparison to other available model organisms, very little work has been devoted to pig proteomics until recently. Keeping this in mind, the present review will highlight some of the advantages and disadvantages of pig as a model system for proteomic studies.
Proteomics in pancreatic cancer research
Authors: Cecconi Daniela , Palmieri Marta , Donadelli Massimo
Published: December 2010

In this review, we give an overview of the actual role of proteomic technologies in the study of pancreatic cancers (PCs). We describe PC proteomics on the basis of sample origins, i.e. tissues, body fluids, and PC cell lines. As regards PC tissues, we report the identification of a number of candidate biomarkers of precursor lesions that may allow early diagnosis of this neoplasia. Moreover, we describe cytoskeletal and hypoxia‐regulated proteins that confirm the involvement of cytoskeleton modifications and metabolism adaptations in carcinogenesis. We also discuss the most important biomarkers identified by proteomic analysis involved in local invasion and distant metastasis, and in the cross‐talk between pancreatic tumor and the surrounding stroma. Furthermore, we report novel candidate biomarkers identified in serum, plasma, and pancreatic juice of cancer patients compared with cancer‐free controls. Proteomic alterations in PC cell line models as compared to normal controls and studies on cell lines treated with drugs or new agents to understand their mechanism of pharmacological action or the onset of drug resistance are also presented. Finally, we discuss the recent improvements obtained in classical 2‐DE and high‐throughput proteomic strategies able to allow the overcoming of relevant proteomic drawbacks.
Counting peptide‐water hydrogen bonds in unfolded proteins
Authors: Gong Haipeng , Porter Lauren L. , Rose George D.
Published: December 2010

It is often assumed that the peptide backbone forms a substantial number of additional hydrogen bonds when a protein unfolds. We challenge that assumption in this article. Early surveys of hydrogen bonding in proteins of known structure typically found that most, but not all, backbone polar groups are satisfied, either by intramolecular partners or by water. When the protein is folded, these groups form approximately two hydrogen bonds per peptide unit, one donor or acceptor for each carbonyl oxygen or amide hydrogen, respectively. But when unfolded, the backbone chain is often believed to form three hydrogen bonds per peptide unit, one partner for each oxygen lone pair or amide hydrogen. This assumption is based on the properties of small model compounds, like N‐methylacetamide, or simply accepted as self‐evident fact. If valid, a chain of N residues would have approximately 2N backbone hydrogen bonds when folded but 3N backbone hydrogen bonds when unfolded, a sufficient difference to overshadow any uncertainties involved in calculating these per‐residue averages. Here, we use exhaustive conformational sampling to monitor the number of H‐bonds in a statistically adequate population of blocked polyalanyl‐six‐mers as the solvent quality ranges from good to poor. Solvent quality is represented by a scalar parameter used to Boltzmann‐weight the population energy. Recent experimental studies show that a repeating (Gly‐Ser) polypeptide undergoes a denaturant‐induced expansion accompanied by breaking intramolecular peptide H‐bonds. Results from our simulations augment this experimental finding by showing that the number of H‐bonds is approximately conserved during such expansion⇋compaction transitions.
A new liquid chromatography/mass spectrometry method for 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanol (NNAL) in urine
Authors: Bhat Showket H. , Gelhaus Stacy L. , Mesaros Clementina , Vachani Anil , Blair Ian A.
Published: December 2010

4‐(Methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone (NNK) is a carcinogenic nitrosamine produced upon curing tobacco. It is present in tobacco smoke and undergoes metabolism to 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanol (NNAL) in the lungs. NNAL undergoes further uridine diphosphate glucuronosyltransferase (UGT)‐mediated metabolism to give N‐ and O‐glucuronide metabolites, which together with free (non‐conjugated) NNAL are then excreted in the urine. The ability to conduct validated analyses of free and conjugated NNAL in human urine is important in order to assess inter‐individual differences in lung cancer risk from exposure to cigarette smoke. The use of stable isotope dilution (SID) methodology in combination with liquid chromatography/multiple reaction monitoring/mass spectrometry (LC/MRM‐MS) provides the highest bioanalytical specificity possible for such analyses. We describe a novel derivatization procedure, which results in the formation of a pre‐ionizedN‐propyl‐NNAL derivative. The increased LC/MS sensitivity arising from this derivative then makes it possible to analyze free NNAL in only 0.25 mL urine. This substantial reduction in urine volume when compared with other methods that have been developed will help preserve the limited amounts of stored urine samples that are available from on‐going longitudinal biomarker studies. The new high sensitivity SID LC/MRM‐MS assay was employed to determine free and conjugated NNAL concentrations in urine samples from 60 individual disease‐free smokers. Effects of inter‐individual differences in urinary creatinine clearance on NNAL concentrations were then assessed and three metabolizer phenotypes were identified in the 60 subjects from the ratio of urinary NNAL glucuronides/free NNAL. Poor metabolizers (PMs, 14 subjects) with a ratio of NNAL glucuronides/free NNAL <2 (mean = 1.3), intermediate metabolizers (IMs, 36 subjects) with a ratio between 2 and 5 (mean = 3.4), and extensive metabolizers (EMs, 10 subjects) with a ratio >5 (mean = 11.1). Copyright © 2010 John Wiley & Sons, Ltd.
Surface‐assisted laser desorption/ionization mass spectrometry with a rotating ball interface
Authors: Alimpiev Sergey , Grechnikov Alexander , Sunner Jan , Karavanskii Vladimir , Simanovsky Yaroslav , Nikiforov Sergey
Published: December 2010

A rotating ball interface for surface‐assisted laser desorption/ionization (SALDI) mass spectrometry was designed and tested. One side of the ball was exposed to atmospheric pressure and the other to the vacuum in a time‐of‐flight mass spectrometer. Analytes (arginine, atenolol, reserpine, tofisopam, and chloropyramine) were applied using electrospray to a silicon substrate on the atmospheric side, the ball was rotated 180°, and the analyte was desorbed on the vacuum side using a pulsed, 200 Hz, 355 nm laser. In order to increase the desorption area, the laser focus was scanned over the substrate in a raster pattern repeated once every second. The design allows for rapid sample throughout with a sample turn‐around time as short as 5 s. Newly produced porous silicon substrates initially yielded very low ion signals, and they required several hundred laser shots to attain maximum sensitivity. In contrast, amorphous silicon did not require such ‘activation’. Quantitative analysis showed a sample‐to‐sample reproducibility of about 10%. The sensitivities with model analytes were in the 1000 to 10 000 ions/fmole range and detection limits in the low fg range. Copyright © 2010 John Wiley & Sons, Ltd.
Fourier transform ion cyclotron resonance cell with dynamic harmonization of the electric field in the whole volume by shaping of the excitation and detection electrode assembly
Authors: Boldin Ivan A. , Nikolaev Eugene N.
Published: December 2010

A new principle of formation of the effective electric field distribution in a Penning trap is presented. It is based on the concept of electric potential space averaging via charged particle cyclotron motion. The method of making hyperbolic‐type field distribution in the whole volume of a cylindrical Penning trap is developed on the basis of this new principal. The method is based on subdividing the cell cylindrical surface into segments with shapes producing quadratic dependence on axial coordinate of an averaged (along cyclotron motion orbit) electric potential at any radius of cyclotron motion. The cell performance is compared in digital experiments with the performance of a Gabrielse‐type cylindrical cell with four compensation electrodes and is shown to be more effective in ion motion harmonization at higher cyclotron radii and axial oscillation amplitude. Copyright © 2010 John Wiley & Sons, Ltd.
Vortex‐assisted tryptic digestion
Authors: Yang Hyo‐Jik , Shin Seongjae , Kim Jinhee , Hong Jangmi , Lee Sunyoung , Kim Jeongkwon
Published: December 2010

The effect of vortex‐induced vibration during tryptic digestion was investigated by applying different vibrational speeds (0, 600, 1200, or 2500 rpm) to digestion solutions for varying durations (10, 20, 30, 40, or 60 min) at two different incubation temperatures (25°C or 37°C). The most rapid digestion was observed with the highest vibrational speed and temperature. With the application of 2500 rpm at 37°C, the tryptic digestion of each of three standard proteins (cytochrome c, myoglobin, or bovine serum albumin) provided complete disappearance of the protein within 60 min, as determined by matrix‐assisted laser desorption/ionization mass spectrometry. Compared to conventional overnight digestion, 60‐min vortex‐assisted tryptic digestion generated longer peptides, due primarily to the limited digestion time and provided better sequence coverages (89% vs. 78% for cytochrome c, 100% vs. 87% for myoglobin, and 38% vs. 26% for BSA). The longer peptides should be advantageous to analytical methods such as the middle‐down approach that benefit from increased sequence coverage of proteins. Vortex‐assisted tryptic digestion is expected to be a useful method for rapid tryptic digestion of proteins. Copyright © 2010 John Wiley & Sons, Ltd.
Highly Controlled Surface‐Enhanced Raman Scattering Chips Using Nanoengineered Gold Blocks
Authors: Yokota Yukie , Ueno Kosei , Misawa Hiroaki
Published: December 2010

Well defined gold nanostructures of various sizes are fabricated on glass substrates using high‐resolution electron‐beam lithography/lift‐off techniques and detailed surface‐enhanced Raman scattering (SERS) properties of crystal violet molecules are studied in order to elucidate electromagnetic (EM) field enhancement effects on the fabricated structures. SERS measurements are performed with high reproducibility using in situ Raman microspectroscopy in aqueous solution. An analysis based on EM theory is performed using field‐enhancement factors obtained from finite‐difference time‐domain (FDTD) simulations and the analysis reproduces experimental results very well. It is noteworthy, furthermore, that the proposed analytic method of EM effects on SERS allows the estimate of the ideal local temperature of gold nanostructures by canceling out the difference in EM field factors at Stokes and anti‐Stokes Raman scattering wavelengths. Thus, these experimental results demonstrate that quantitative analysis based on EM theory can be obtained using highly controlled gold nanostructures for SERS measurements with high reproducibility, a result that is promising for the construction of a SERS analysis chip. Although no SERS chip reported so far has been usable for quantitative analysis, this study opens the door for construction of a quantitative SERS chip.