bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptotic expansions of multiply scattered surface currents
Authors: Ecevit Fatih 
Published: February 2008

AbstractWe have recently uncovered the convergence characteristics of multiple scattering iterations for “two‐dimensional” as well as “three‐dimensional scalar (acoustics)” scattering models in the high‐frequency regime. As we have demonstrated, a most distinctive property of these latermodels, compared to their two‐dimensional counterparts, is the dependence of corresponding asymptotic expansions on the relative angle of rotation between the principal axes of the successive reflection points of the optical rays. Concerning the case of fully “three‐dimensional vector (electromagnetic)” scattering problems, here we show that the vectorial nature of the problem, in turn, gives rise to new additional complex structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Equation‐free methods for molecular dynamics: a lifting procedure
Authors: Frederix Yves , Samaey Giovanni , Vandekerckhove Christophe , Roose Dirk 
Published: February 2008

AbstractWe present a lifting procedure for the initialization of molecular dynamics simulations of dense fluids in the context of equation‐free computing. As the macroscopic system description we use a smooth representation of the density and velocity profile using a kernel density estimation, of which the dimensionality is reduced via a spline fit. The proposed initialization procedure generates initial atom positions on a grid, as well as initial velocities, such that the desired macroscopic density and velocity profiles are well approximated. We illustrate the approach on a model problem, and point out some inherent caveats in the design of good lifting operators for molecular dynamics. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of the Alzheimer's disease amyloid precursor protein (APP) and its homologue APLP2 as essential modulators of glucose and insulin homeostasis and growth
Authors: Needham BE , Wlodek ME , Ciccotosto GD , Fam BC , Masters CL , Proietto J , Andrikopoulos S , Cappai R 
Published: February 2008

AbstractThe amyloid precursor protein (APP), the source of the neurotoxic amyloid β (Aβ) peptide involved in Alzheimer's disease (AD), belongs to a conserved family of related proteins. In mammals, the APP family contains amyloid precursor‐like protein 1 (APLP1) and amyloid precursor‐like protein 2 (APLP2). Whilst a number of activities have been attributed to the APP family, an overall function has not been definitively established. While ablating either the APP or APLP2 gene in mice produces minimal phenotypic change, the combined knockout of these genes in mice causes postnatal mortality. Postnatal survival therefore requires a shared but unknown function of APP and APLP2. To investigate the biochemical basis for the postnatal lethality, plasma was analysed from double knockout mice (APP−/− APLP2−/−) 2 days before birth, at gestational day E17, and from mice at 12–16 h after birth. The postnatal double knockouts had 66% lower plasma glucose levels than their wild‐type controls and 50% lower than their single knockout counterparts. Interestingly, the postnatal double knockouts displayed hyperinsulinaemia, as shown by inappropriate plasma insulin levels, given their degree of hypoglycaemia. The single knockout mice also showed hyperinsulinaemia and had 31% lower plasma glucose than the wild‐types. While the double knockouts did not survive more than 24 h after birth, the single knockouts reached adulthood and their hypoglycaemia continued. Therefore, APP and APLP2 expression modulates plasma insulin and glucose concentrations. Plasma calcium, magnesium and phosphate were also significantly reduced in the double knockouts compared to the wild‐types, and they showed distinctive growth restriction, suggesting the involvement of a metabolic impairment. These results link the expression of the APP and APLP2 genes with glucose homeostasis and growth and therefore identify a novel function for the APP family. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation
Authors: Mikulík Karel , Palečková Petra , Felsberg Jürgen , Bobek Jan , Zídková Jarmila , Halada Petr 
Published: February 2008

AbstractTransfer‐messenger RNA (tmRNA, 10Sa RNA, ssrA) is bacterial RNA having both tRNA and mRNA properties and playing an essential role in recycling of 70S ribosomes that are stalled on defective mRNA. The trans‐translational system is thought to play a crucial role in bacterial survival under adverse conditions. Streptomycetes are Gram‐positive soil bacteria exposed to various physical and chemical stresses that activate specialized responses such as synthesis of antibiotics and morphological differentiation. Comparative sequence analysis of ssrA genes of streptomycetes revealed the most significant differences in the central parts of tag‐reading frames, in the stop codons and in the 15–34 nucleotide sequences following stop codons. A major challenge in understanding the interactions that control the function of tmRNA is the definition of protein interactions. Proteins from various phases of development of Streptomyces aureofaciens associated with tmRNA were analyzed. Using affinity chromatography on tmRNA‐Sepharose and photo cross‐linking experiments with [32P]labeled tmRNA seven proteins, the β and β′‐subunits of DNA dependent RNA polymerase, polyribonucleotide nucleotidyltransferase (PNPase), ribosomal protein SS1, ATP‐binding cassette transporters, elongation factor Tu, and SmpB were identified among the proteins associated with tmRNA of S. aureofaciens. We examined the functional role of ribosomal protein SS1 in a defined in vitro trans‐translation system. Our data show that the protein SS1 that structurally differs from S1 of Escherichia coli is required for translation of the tmRNA tag‐reading frame.
The origin and control of ex vivo oxidative peptide modifications prior to mass spectrometry analysis
Authors: Froelich Jennifer M. , Reid Gavin E. 
Published: February 2008

AbstractThe origin and control of ex vivo sample handling related oxidative modifications of methionine‐, S‐alkyl cysteine‐, and tryptophan‐containing peptides obtained from typical “in‐solution” or “in‐gel” proteolytic digestion strategies, have been examined by capillary HPLC and MS/MS. The origin of increased oxidation levels were found to be predominantly associated with the extensive ex vivo sample handling steps required for gel electrophoresis and/or in‐gel proteolytic digestion of proteins prior to analysis by MS. Conditions for deliberately controlling the oxidation state (both oxidation and reduction) of these peptides, as well as for those containing cysteine, have been evaluated using a series of model synthetic peptides and standard tryptic protein digests. Essentially complete oxidation of methionine‐ and S‐alkyl cysteine‐containing peptides was achieved by reaction with 30% hydrogen peroxide/5% acetic acid at room temperature for 30 min. Under these conditions, cysteine was also converted to cysteic acid, while only limited oxidation of tryptophan to oxindolylalanine, and methionine and S‐alkyl cysteine sulfoxides to their respective sulfones, were observed. Efficient reduction of methionine‐ and S‐alkyl cysteine sulfoxide‐containing peptides was achieved by reaction in 1 M dimethylsulfide/10 M hydrochloric acid at room temperature for 10 and 45 min, respectively. None of the reduction conditions evaluated were found to result in the reduction of oxindolylalanine, cysteic acid, or methionine sulfone.
Reduced airway function in early adulthood among subjects with wheezing disorder before two years of age
Authors: Goksör Emma , Gustafsson Per M , Alm Bernt , Åmark Mainor , Wennergren Göran 
Published: February 2008

AbstractAimTo compare airway function in early adulthood in subjects with wheezing in infancy with age‐matched controls and to analyze what accounts for a possible difference.MethodsAsthma development has been prospectively studied in 101 children hospitalized due to wheezing before the age of two. The cohort was re‐investigated at age 17–20 years and tested with spirometry and for bronchial hyper‐responsiveness and allergic sensitization. An age‐matched population (n = 294) was used for comparison.ResultsThe cohort had a significantly lower FEV1/FVC ratio and MEF50, both pre‐ and post‐bronchodilation, compared with the controls, P < 0.01. The reduction in airway function was most evident in current asthmatic female subjects, but a reduced pre‐bronchodilation FEV1/FVC ratio was also seen in symptom‐free cohort subjects, P = 0.03. In the multivariate analysis, female gender was the most prominent independent risk factor for reduced airway function in early adulthood, pre‐bronchodilation OR 4.0 (1.4–11.3) and post‐bronchodilation OR 8.8 (1.8–42.0). In addition, a history of early wheezing, that is, belonging to the cohort, was an independent risk factor for reduced airway function pre‐bronchodilation, OR 3.3 (1.3–8.7). Furthermore, there was an association between current bronchial hyper‐responsiveness and an increased risk of reduced airway function post‐bronchodilation, OR 7.3 (2.0–26.6).ConclusionReduced airway function in early adulthood was found in subjects with wheezing early in life, compared with age‐matched controls. The reduction was most prominent in females with current asthma. Pediatr Pulmonol. 2008; 43:396–403. © 2008 Wiley‐Liss, Inc.
Isotopic evidence for condensed aromatics from non‐pyrogenic sources in soils – implications for current methods for quantifying soil black carbon
Authors: Glaser Bruno , Knorr Klaus‐Holger 
Published: February 2008

AbstractBlack carbon (BC) is a complex continuum of partly charred organic matter predominantly consisting of condensed aromatic and graphitic moieties and it has high potential for long‐term carbon sequestration in soils and sediments. There has been common agreement that BC is exclusively formed by incomplete combustion of organic matter, while non‐pyrogenic sources are negligible. In this study, we investigated the stable carbon isotope signature of benzenepolycarboxylic acids (BPCAs) as molecular markers for BC to test if there is also a significant contribution of non‐pyrogenic carbon to this fraction in soils. BPCAs were formed by hot nitric acid oxidation of different soils and analyzed by three different procedures: (i) elemental analysis – isotope ratio mass spectrometry (EA‐IRMS) of bulk BPCAs and gas chromatography – combustion – isotope ratio mass spectrometry (GC‐C‐IRMS) of (ii) BPCA trimethylsilyl (TMS) derivatives, and (iii) BPCA methyl derivatives. Best accuracy and precision of isotope measurements were obtained by EA‐IRMS of bulk BPCAs although this method has a risk of contamination by non‐BC‐derived compounds. The accuracy and precision of GC‐C‐IRMS measurements were superior for methyl derivatives (±0.1‰ and 0.5‰, respectively) to those for TMS derivatives (+3.5‰ and 2.2‰, respectively).Comparison of BPCA δ13C values of soil samples prior to and after laboratory and field incubations with both positive and negative 13C labels at natural and artificial abundances revealed that up to 25% of the isolated BC fraction in soils had been produced in situ, without fire or charring. Commonly applied methods to quantify BC exclusively formed by pyrogenic processes may thus be biased by a significant non‐pyrogenic fraction. Further research is encouraged to better define isolated BC fractions and/or understand mechanisms for non‐pyrogenic BC production in soils. Copyright © 2008 John Wiley & Sons, Ltd.
A model to predict outbreak periods of the pest blackfly Simulium chutteri Lewis (simuliidae, Diptera) in the Great Fish River, Eastern Cape province, South Africa
Authors: Rivers‐Moore N. A. , Hughes D. A. , de Moor F. C. 
Published: February 2008

AbstractElevated, more constant flows characterize the current flow regime of the Great Fish River (Eastern Cape province, South Africa) following the completion of an interbasin transfer scheme (IBT) in 1977, where prior to this the winter months were often characterized by zero flows. Changes in aquatic macroinvertebrate communities, and in particular outbreaks of the pest blackfly Simulium chutteri Lewis (Diptera: Simuliidae) have been documented in response to these altered flows. Integrated control measures of pest blackfly have been advocated based on flow reductions during the winter months. In this study, a site‐specific discharge threshold of 2 m3 s−1 was identified as a flow reduction target based on the amount of hydraulic habitat available to S. chutteri larvae within a particular rapid. Hydrological analyses showed that flow conditions have created ideal blackfly larval habitat in this rapid, with prolonged uninterupted periods (>3 months) exceeding this threshold. A model was developed to predict probabilities and severities of blackfly outbreaks, based on flow periods and water temperatures, both of which determine the success and duration respectively of the aquatic phase of S. chutteri. July was identified as the critical month for flow restriction to 2 m3 s−1 for a period of 38 days, in order to reduce the winter populations of S. chutteri in the Great Fish River at the study site and avoid the typical spring outbreaks of blackfly. Copyright © 2008 John Wiley & Sons, Ltd.
Optimum fish passage and guidance designs are based in the hydrogeomorphology of natural rivers
Authors: Nestler J. M. , Goodwin R. A. , Smith D. L. , Anderson J. J. , Li S. 
Published: February 2008

AbstractUnderstanding hydrodynamic cues used by outmigrating juvenile salmon (emigrants) to guide fine‐scale swim path selection is critical to successful fish guidance and passage at man‐made structures. We show how these cues can be inferred from channel features and complex flow fields of natural rivers through which emigrants pass. We then describe a new cue, ‘total hydraulic strain’, integrating properties of flow acceleration and turbulence through the spatial gradients in velocity to create a single flow field distortion metric amenable to the analysis of fish movement at the scale of large man‐made structures. We explain how total hydraulic strain, together with the magnitude of velocity, provide sufficient information for any fish to distinguish between the two categories of channel features with their mechanosensory system. We demonstrate that total hydraulic strain, velocity magnitude and hydrostatic pressure can be integrated into rule‐sets (the Strain–Velocity–Pressure (SVP) Hypothesis) to explain emigrant swim path selection near dams. To confirm the reasonableness of the SVP Hypothesis, we describe how its separate elements can be detected by different components of the fish mechanosensory system. We evaluate the SVP Hypothesis by (1) using it to explain the traces made by acoustically tagged emigrants overlaid on coincident total hydraulic strain and velocity magnitude fields, (2) using it to explain different passage efficiencies of competing bypass designs and (3) testing it via stepwise discriminant analysis to infer the relationship between hydrodynamic pattern and emigrant orientation. We conclude the SVP Hypothesis is a reasonable and useful approximation of the strategy used by emigrants to select their swim path through complex flow fields sufficient to serve as the basis of guidance and bypass system design. Published in 2008 by John Wiley & Sons, Ltd.
The security and improvement of an ultra‐lightweight RFID authentication protocol
Authors: Li Tieyan , Deng Robert H. , Wang Guilin 
Published: February 2008

AbstractIt is very challenging on designing cryptographically strong security functions that can be incorporated into low‐cost radio frequency identification (RFID) tags. Some RFID authentication protocols were proposed using only ultra‐lightweight primitives, while the security of them must be scrutinized before being put forth into any real application. In this paper, we present two effective attacks, namelyde‐synchronization attackandfull‐disclosure attack, against an efficient ultra‐lightweight RFID mutual authentication protocol: LMAP2, which is recently proposed by Peris‐Lopezet al. These active attacks are so serious as they cannot only disable the authentication capability of an RFID tag by destroying synchronization between the tag and the RFID reader, but also disclose all secret values stored in the tag. We point out the design flaws of the protocol and based on that, we improve the protocol with a stateful variant (SLMAP). The improved protocol is more secure in sense of tag anonymity, man‐in‐the‐middle (MITM) resistance, and forgery prevention as shown in our analysis, and is more compact due to reduced operations and memory usage on implementing such a tag. Copyright © 2008 John Wiley & Sons, Ltd.
Designing fault tolerant networks to prevent poison message failure
Authors: Du Xiaojiang , Shayman Mark A. , Skoog Ronald A. 
Published: February 2008

AbstractPoison message failure is a mechanism that has been responsible for large‐scale failures in both telecommunications and IP networks. We design a fault management framework that integrates passive diagnosis and active diagnosis to identify the poison message and prevent network instability. Passive diagnosis uses real‐time inference and reasoning techniques to analyze network information and generates a probability distribution of the poison message, and the probability distribution is used in active diagnosis for further failure identification. In active diagnosis, message filtering is used to block suspect message types. Blocking messages affects network performance and service. The tradeoff of message filtering is formulated as a Markov Decision Process (MDP). The large size of the state space makes it impractical to use traditional techniques to solve the MDP. Con sequently, we use a combination of reinforcement learning and feature‐based function approximation to obtain a suboptimal policy. Extensive simulations demonstrate the effectiveness of passive diagnosis, and show that the suboptimal policy performs significantly better than a well‐known heuristic policy. Copyright © 2008 John Wiley & Sons, Ltd.
Ultraviolet femtosecond laser ionization mass spectrometry
Authors: Imasaka Totaro 
Published: February 2008

AbstractFor this study, multiphoton ionization/mass spectrometry using an ultraviolet (UV) femtosecond laser was employed for the trace analysis of organic compounds. Some of the molecules, such as dioxins, contain several chlorine atoms and have short excited‐state lifetimes due to a “heavy atom” effect. A UV femtosecond laser is, then, useful for efficient resonance excitation and subsequent ionization. A technique of multiphoton ionization using an extremely short laser pulse (e.g., <10 fs), referred to as “impulsive ionization,” may have a potential for use in fragmentation‐free ionization, thus providing information on molecular weight in mass spectrometry. © 2008 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 8: 23–32; 2008: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20136
Polyisoprenoid alcohols—Recent results of structural studies
Authors: Skorupinska‐Tudek Karolina , Wojcik Jacek , Swiezewska Ewa 
Published: February 2008

AbstractPolyisoprenoid alcohols (polyprenols and dolichols) are linear polymers of from several up to more than 100 isoprene units identified in almost all living organisms. Studies of their chemical structures have resulted in the discovery of new variants such as the recently described alloprenols with reversed configuration of the double bond in the α‐isoprene unit. In parallel, structural elucidation of metabolically labeled plant dolichols has indicated that both the mevalonate and methylerythritol phosphate pathways are involved in the biosynthesis of dolichols in roots, leading to the construction of a spatial model of their biosynthesis. According to this model, in root cells, synthesis of the dolichol molecule is initiated in the plastids, and the resulting intermediates, oligoprenyl diphosphates, are exported to the cytoplasm and are elongated up to the desired chain length. The metabolic consequences of this putative model are discussed in the context of the enzymatic machinery involved. © 2008 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 8: 33–45; 2008: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20137
Identification of an NADH‐dependent 5‐hydroxymethylfurfural‐reducing alcohol dehydrogenase in Saccharomyces cerevisiae
Authors: Laadan Boaz , Almeida João R. M. , Rådström Peter , Hahn‐Hägerdal Bärbel , Gorwa‐Grauslund Marie 
Published: February 2008

AbstractWe report on the identification and characterization of a mutated alcohol dehydrogenase 1 from the industrial Saccharomyces cerevisiae strain TMB3000 that mediates the NADH‐dependent reduction of 5‐hydroxymethylfurfural (HMF) to 2,5‐bis‐hydroxymethylfuran. The co‐factor preference distinguished this alcohol dehydrogenase from the previously reported NADPH‐dependent S. cerevisiae HMF alcohol dehydrogenase Adh6. The amino acid sequence revealed three novel mutations (S109P, L116S and Y294C) that were all predicted at the vicinity of the substrate binding site, which could explain the unusual substrate specificity. Increased biomass production and HMF conversion rate were achieved in a CEN.PK S. cerevisiae strain overexpressing the mutated ADH1 gene. Copyright © 2008 John Wiley & Sons, Ltd.
Minimally Invasive Video‐Assisted Thyroidectomy for Benign Thyroid Disease: An Evidence‐Based Review
Authors: Miccoli Paolo , Minuto Michele N. , Ugolini Clara , Pisano Roberta , Fosso Alessandra , Berti Piero 
Published: February 2008

AbstractBackgroundA decade after nearly all surgical disciplines developed minimally invasive techniques, the first report of a single case of minimally invasive thyroidectomy was published. Minimally invasive video‐assisted thyroidectomy (MIVAT) is now considered the most widely practiced and most easily reproducible minimally invasive procedure for thyroidectomy. The aim of this review was to analyze the treatment of benign thyroid diseases by MIVAT.MethodsA systematic evidence‐based literature review focusing on three questions was carried out. Additional data were obtained on the basis of our personal experience. (1) Are minimally invasive procedures indicated in the treatment of thyroid diseases? (2) Is MIVAT a safe technique and what are the demonstrated advantages? (3) Since different thyroid diseases may be treated by MIVAT, is it of any value in the treatment of benign thyroid diseases?ResultsMIVAT can be considered an appropriate treatment of some thyroid diseases; it represents a safe procedure with the same incidence of complications as traditional surgery, and also has advantages in terms of both cosmetic result and postoperative distress.ConclusionsIn spite of an increasing trend toward performing more extensive procedures other than thyroidectomy alone during videoscopic procedures, the current literature seems to reaffirm that the main and safest indication for MIVAT is benign disease.