bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of mouse inbred strains through mitochondrial DNA single‐nucleotide extension
Authors: Goios Ana , Gusmão Leonor , Rocha Ana Mafalda , Fonseca Amélia , Pereira Luísa , Bogue Molly , Amorim António 
Published: December 2008

AbstractInbred mouse strains are used as model organisms for biomedical research in laboratories throughout the world. The most widely used of these strains had their genome sequenced recently, and phylogenetic studies have been performed, namely, based on mitochondrial DNA (mtDNA). This has allowed determining that few polymorphisms distinguish the mtDNAs of the common inbred strains, but a high number of differences are observed among the wild‐derived strains. Taking advantage of these observations, we here present a single base extension typing strategy that, with only a pair of multiplex reactions, allows the distinction between common inbred and wild‐derived mice strains, and provides the identification of ten different common inbred and six wild‐derived mice mtDNA haplotypes. Given that all the animals inside a strain present the same mtDNA, this strategy allows a rapid identification of the strains without the need for probability calculations. We further test this approach in an island population of wild mice, which provides both an indication on its applicability in wild mice, and a comparison of evolutionary processes on inbred and wild mice that are restricted to a limited space. Rapid genotyping methods that allow the distinction of the different strains are important for both the distinction of materials such as tissue and cell collections and to identify the origin of new strains. Moreover, it may also prove valuable in forensic identification of materials collected in laboratory accidents, as well as in cases of scientific fraud.
Strategies for enhancing the speed and integration of microchip genetic amplification
Authors: Hoang Viet N. , Kaigala Govind V. , Atrazhev Alexey , Pilarski Linda M. , Backhouse Christopher J. 
Published: December 2008

AbstractIn this work, we explore the use of methods that allow a significant acceleration of genetic analysis within microchips fabricated from low thermal conductivity materials such as glass or polymers. Although these materials are highly suitable for integrating a number of genetic analysis techniques onto lab‐on‐a‐chip devices, their low thermal conductivity limits the rate at which heat can be transferred and hence lowers the speed of thermal cycling. However, short thermal cycling times are the key to bringing PCR to clinical point‐of‐care applications. Although shrinking the PCR reaction chamber volume can increase the speed of thermal cycling, this strategy is not always suitable, particularly when dealing with clinical samples with low analyte concentrations. In the present work, we combine two alternate strategies for decreasing the time required to perform PCR: implementing a heat sink and optimizing the PCR protocol. First, the heat sink substantially reduces the thermal resistance opposing heat dissipation into the ambient environment, and eliminates the parasitic thermal capacitance of the regions in the microchip that do not require heating. The low thermal conductivity of glass is used to our advantage to design the heat‐sink placement to achieve fast thermal transitions while maintaining low power consumption. Second, we explore the application of two‐stage PCR to provide a further reduction in the time required to perform genetic amplification by merging the annealing and extension stages of the commonly used three‐stage PCR approach. In combination, we reduce the time required to perform thermal cycling by roughly a factor of 3 while improving the temperature control.
DNA sequencing by microchip electrophoresis using mixtures of high‐ and low‐molar mass poly(N,N‐dimethylacrylamide) matrices
Authors: Hert Daniel G. , Fredlake Christopher P. , Barron Annelise E. 
Published: December 2008

AbstractPrevious studies have reported that mixed molar mass polymer matrices show enhanced DNA sequencing fragment separation compared with matrices formulated from a single average molar mass. Here, we describe a systematic study to investigate the effects of varying the amounts of two different average molar mass polymers on the DNA sequencing ability of poly(N,N‐dimethylacrylamide) (pDMA) sequencing matrices in microfluidic chips. Two polydisperse samples of pDMA, with weight‐average molar masses of 3.5 MDa and 770 kDa, were mixed at various fractional concentrations while maintaining the overall polymer concentration at 5% w/v. We show that although the separation of short DNA fragments depends strongly on the overall solution concentration of the polymer, inclusion of the high‐molar mass polymer is essential to achieve read lengths of interest (>400 bases) for many sequencing applications. Our results also show that one of the blended matrices, comprised of 3% 3.5 MDa pDMA and 2% 770 kDa pDMA, yields similar sequencing read lengths (>520 bases on average) to the high‐molar mass matrix alone, while also providing a fivefold reduction in zero‐shear viscosity. These results indicate that the long read lengths achieved in a viscous, high‐molar mass polymer matrix are also possible to achieve in a tuned, blended matrix of high‐ and low‐molar mass polymers with a much lower overall solution viscosity.
Development of an entangled polymer solution for improved resolution in DNA typing by CE
Authors: Boulos Stefano , Cabrices Oscar , Blas Maximilien , McCord Bruce R. 
Published: December 2008

AbstractA new sieving matrix consisting of a mixture of two commercial polymers with different chemical structures, PVP (Mw=1 000 000 g/mol) and hydroxyethyl cellulose (HEC, Mw=250 000 g/mol), has been successfully used for single‐stranded DNA separation. This sieving matrix was optimized with a Doehlert design, a second‐order model statistical design. A total concentration of 3.5% of polymer, which contains 20.4% of PVP relative to HEC, combines the superior coating capability of the PVP with the high efficiency of the HEC. The use of this new sieving matrix gives highly resolved and reproducible separations of single‐stranded DNA ranging from 50 to 500 bp. The separation of these DNA fragments is accomplished in less than 30 min under 319 V/cm with efficiencies up to 4 million plates per meter (measured at 350 bp). More than 90 successive analyses were achieved without any deterioration of the separation performance. Repeatability values of resolution (given as %RSD) for the analyzed DNA fragments are 2.2% (measured with the couple 139/150 bp) and 5.3% (measured with the couple 490/500 bp). Moreover, this mixture has a low viscosity (388 cP), which permits easy filling of fused‐silica capillaries. This new sieving matrix, which exhibits high sieving performance, good dynamic coating ability, and low viscosity, can be a useful alternative to other less easily synthesized sieving matrices and eliminates the need for precoating the capillary to eliminate electroosmosis.
An arbitrary Lagrangian–Eulerian method based on the adaptive Riemann solvers for general equations of state
Authors: Tian Baolin , Shen Weidong , Jiang Song , Wang Shuanghu , Liu Yan 
Published: December 2008

AbstractApproximate or exact Riemann solvers play a key role in Godunov‐type methods. In this paper, three approximate Riemann solvers, the MFCAV, DKWZ and weak wave approximation method schemes, are investigated through numerical experiments, and their numerical features, such as the resolution for shock and contact waves, are analyzed and compared. Based on the analysis, two new adaptive Riemann solvers for general equations of state are proposed, which can resolve both shock and contact waves well. As a result, an ALE method based on the adaptive Riemann solvers is formulated. A number of numerical experiments show good performance of the adaptive solvers in resolving both shock waves and contact discontinuities. Copyright © 2008 John Wiley & Sons, Ltd.
Risk factor beta conditional value‐at‐risk
Authors: Semenov Andrei 
Published: December 2008

AbstractWe propose a new approach to the estimation of the portfolio Value‐at‐Risk. Based on the assumption that the same macroeconomic factors affect returns of all assets in a portfolio, this methodology allows the generation of the sequence of hypothetical future equilibrium portfolio returns given the historical values of the underlying macroeconomic factors and the asset betas with respect to these factors. Value‐at‐Risk is then found as an appropriate percentile of the corresponding hypothetical distribution of the portfolio profits and losses. The backtesting results for the six Fama–French benchmark portfolios and the S&P500 index show that this approach yields reasonably accurate estimates of the portfolio Value‐at‐Risk. Copyright © 2008 John Wiley & Sons, Ltd.
The DEAD‐box RNA helicase DDX1 interacts with RelA and enhances nuclear factor kappaB‐mediated transcription
Authors: Ishaq Musarat , Ma Li , Wu Xiaoyun , Mu Yongxin , Pan Ji'an , Hu Jiajie , Hu Tao , Fu Qiong , Guo Deyin 
Published: December 2008

AbstractDEAD‐box RNA helicases constitute the largest family of RNA helicases and are involved in many aspects of RNA metabolism. In this study, we identified RelA (p65), a subunit of nuclear factor‐kappaB (NF‐κB), as a cellular co‐factor of DEAD‐box RNA helicase DDX1, through mammalian two hybrid system and co‐immunoprecipitation assay. Additionally, confocal microscopy and chromatin immunoprecipitation assays confirmed this interaction. In NF‐κB dependent reporter gene assay, DDX1 acted as a co‐activator to enhance NF‐κB‐mediated transcription activation. The functional domains involved were mapped to the carboxy terminal transactivation domain of RelA and the amino terminal ATPase/helicase domain of DDX1. The DDX1 trans‐dominant negative mutant lacking ATP‐dependent RNA helicase activity lost it transcriptional inducer activity. Moreover, depletion of endogenous DDX1 by specific small interfering RNAs significantly reduced NF‐κB‐dependent transcription. Taken together, the results suggest that DDX1 may play an important role in NF‐κB‐mediated transactivation, and revelation of this regulatory pathway may help to explore the novel mechanisms for regulating NF‐κB transcriptional activity. J. Cell. Biochem. 106: 296–305, 2009. © 2008 Wiley‐Liss, Inc.
GenoMass ‐ a computer software for automated identification of oligonucleotide DNA adducts from LC‐MS analysis of DNA digests
Authors: Liao Qing , Shen Chang , Vouros Paul 
Published: December 2008

AbstractIn the investigation of oligonucleotides, DNA and their adducts by LC‐MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a ‘reversed pseudo‐combinatorial’ approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC‐MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites. Copyright © 2008 John Wiley & Sons, Ltd.
Separation and determination of seleno amino acids using gas chromatography hyphenated with inductively coupled plasma mass spectrometry after hollow fiber liquid phase microextraction
Authors: Duan Jiankun , Hu Bin 
Published: December 2008

AbstractA new derivatization–extraction method for preconcentration of seleno amino acids using hollow fiber liquid phase microextraction (HF‐LPME) was developed for the separation and determination of seleno amino acids in biological samples by gas chromatography–inductively coupled plasma mass spectrometry (GC–ICP‐MS). Derivatization was performed with ethyl chloroformate (ECF) to improve the volatility of seleno amino acids. Parameters influencing microextraction, including extraction solvent, pH of sample solution, extraction time, stirring speed, and inorganic salt concentration have been investigated. Under the optimal conditions, the limits of detection (LODs) obtained for Se‐methyl‐selenocysteine (SeMeCys), selenomethionine (SeMet), and selenoethionine (SeEth) were 23, 15, and 11 ng Se l−1, respectively. The relative standard deviations (RSDs) were 14.6%, 16.4%, and 19.4% for SeMeCys, SeMet, and SeEth (c = 1.0 ng ml−1, n = 7), respectively, and the RSDs for SeMeCys, SeMet could be improved obviously if SeEth was utilized as the internal standard. The proposed method was applied for the determination of seleno amino acids in extracts of garlic, cabbage, and mushroom samples, and the recoveries for the spiked samples were in the range of 96.8–108% and 93.4–115% with and without the use of SeEth as internal standard. The developed method was also applied to the analysis of SeMet in a certified reference material of SELM‐1 yeast and the determined value is in good agreement with the certified value. Copyright © 2008 John Wiley & Sons, Ltd.
Simple radiative models for surface warming and upper‐troposphere cooling
Authors: Keating P. N. 
Published: December 2008

AbstractA simple model of greenhouse‐gas radiative processes intended to make the surface‐warming effect of water‐vapour and CO2 absorption more readily understandable leads to a conclusion that the greenhouse gases also cool the upper troposphere. The results from the simple model are compared with experimental observations, and a functional form for the decline of vertical convection and water‐vapour radiation near the tropopause is derived from previously unexplained high‐altitude cooling‐trend data. A possible reason why global climate models do not show the observed upper‐troposphere cooling trend is tentatively suggested. Copyright © 2008 Royal Meteorological Society
“If only the chronically poor could talk”: listening to voices in poverty from Zambia
Authors: Muuka Gerry Nkombo , Choongo Mutinta Milimo 
Published: December 2008

Abstract

This paper examines the marketing of poverty reduction against twin backdrops, one global the other local: The Millennium Development Goals (MDGs), whose focus is the reduction of human poverty; and poverty in one “developing” economy, Zambia. The paper links marketing to a wider literature in development studies, including a stakeholder coverage that recognizes voices of the poor (Narayan et al., 2000a, b). Voice is arguably a central input to good governance by and within donor agencies, including their social marketing arms. Poverty marketing has at least four key functional elements (after Borden, 1964): Marketing Product, which in Zambia's case is largely agricultural, plus frequently both organic and small‐hold; Marketing Price, which in this case is listening to the “bottom of the pyramid” (Prahalad, 2005); Marketing Place, for example via poverty reduction strategy papers (PSRPs), which must include the local community; and Marketing Promotion, which includes promoting rural infrastructure projects at politicians, to bring entrepreneurial spirit to market. These “4Ps” of Poverty marketing are probably not confined to Zambia. Many “developing” economies present a similar if not overlapping series of strengths, weaknesses, opportunities, and threats. Meeting the challenges to halve extreme poverty by 2015 will require a substantive contribution from both the marketing profession and its arguably fit‐for‐purpose discipline base.

Copyright © 2008 John Wiley & Sons, Ltd.
Second‐gift behaviour of first‐time donors to charity: an empirical study
Authors: Bennett Roger , Ali‐Choudhury Rehnuma 
Published: December 2008

AbstractThis study examined the second‐time charity giving behaviour of a sample of 551 young people during a 2‐year period following the occurrence of their first ever significant donation. It explored the factors that encouraged an individual to make a second gift, the probabilities that a donation would be made within certain time intervals after the initial gift (3 months, 6 months, a year, etc.) and the variables that influenced whether the second donation would go to the charity receiving the person's first gift or to a different charity. Relevant issues were investigatedviaa Cox proportional hazards regression analysis and through a binary logistic regression. Covariates employed in the course of the study included the degree of emotional uplift a person experienced and the level of mind‐set change that took place consequent to a first donation, donor confusion with the range and variety of charities available and the reputation and image congruity of the second charity to which the participant had contributed. The roles of personal inertia and social pressure when making donation decisions were also examined.Copyright © 2008 John Wiley & Sons, Ltd.
Dynamic mechanical analysis of thermotropic copolyester—short glass fiber composites
Authors: Romo‐Uribe Angel , Alvarado‐Tenorio Bonifacio , Romero‐Guzmán Maria Eugenia , Rejón L. , Saldivar‐Guerrero Rubén 
Published: December 2008

AbstractThe influence of short glass fibers (SGF) on the dynamic mechanical properties and microstructure of thermotropic copolyesters based on 1,4‐hydroxybenzoic acid and 2,6‐hydroxynaphthoic acid (denoted B‐N) has been investigated. The mechanical relaxations of the reinforced B‐N/SGF composites were studied under torsion mode and the results were correlated with the degree of molecular alignment and degree of crystallinity as revealed by wide‐angle X‐ray scattering (WAXS). Addition of SGFs to B‐N liquid crystalline polymer (LCP) produced an increase in the solid‐to‐nematic transition temperature as well as an increase in the decomposition temperatures. Dynamic mechanical analysis (DMA) showed that the local motions associated with the β‐transition (∼61°C) are enhanced as the frequency of oscillation increases, i.e. the tan δ maximum increases at higher frequencies. On the other hand, the cooperative motions associated with the α‐transition (∼100°C) are decreased at higher frequencies. The addition of SGF reduced significantly the strength of the α‐transition. Thus, the cooperative molecular motions involving segments of the molecular chains associated with the α‐transition were compromised by the presence of SGFs resulting in an increase of the storage modulus, melting, and degradation temperatures. X‐ray scattering showed that the SGFs disrupted the degree of molecular alignment (as quantified by the order parameter $\bar P_2 $), $\bar P_2 $, and the degree of crystallinity in the composites decreased as the concentration of SGFs increased. Thus, it is suggested that the increase in storage modulus in the composites is attributed to the contribution of the SGFs. Copyright © 2008 John Wiley & Sons, Ltd.
Influence of a terpolymer compatibilizer on the nanostructure of poly(trimethylene terephthalate)/montmorillonite nanocomposites
Authors: Favaro Márcia M. , Branciforti Márcia C. , Bretas Rosario E. S. 
Published: December 2008

AbstractThe use of a compatibilizer to improve the interactions between poly(trimethylene terephthalate) (PTT) and an organically treated montmorillonite (MMT) clay was studied. Nanocomposites, with and without compatibilizer, were obtained using a torque rheometer; their nanostructures were analyzed by wide angle X‐ray diffraction (WAXD), transmission electron microscopy (TEM), steady state and dynamic rheological measurements, and Fourier transform infrared analysis (FT‐IR). Only intercalated structures were obtained when no compatibilizer was added, independent of the mixing method (one or two steps); when the compatibilizer was added, however, intercalated and exfoliated structures were obtained, depending on the masterbatch composition. When the PTT was not present in the masterbatch, two‐phase exfoliated structures were obtained, with a disperse phase composed of nanoclay's lamellas and reticulated compatibilizer and a matrix phase composed of PTT. The compatibilizer cured due to the presence of the nanoclay's surfactant; a mechanism of cure was proposed in which the epoxide rings of the compatibilizer reacted with the hydroxyl groups of the nanoclay's surfactant, forming ether cross‐linkages. It was also concluded that in order to obtain one‐phase exfoliated structures the two steps mixing method using a masterbatch composition of 50 wt% of PTT, 25 wt% of compatibilizer, and 25 wt% of nanoclay gave the best results; after further dilution in the PTT, an exfoliated nanocomposite with a final concentration of 5 wt% of compatibilizer and 5 wt% of nanoclay was obtained. Copyright © 2008 John Wiley & Sons, Ltd.
NetPhosBac – A predictor for Ser/Thr phosphorylation sites in bacterial proteins
Authors: Miller Martin Lee , Soufi Boumediene , Jers Carsten , Blom Nikolaj , Macek Boris , Mijakovic Ivan 
Published: December 2008

AbstractThere is ample evidence for the involvement of protein phosphorylation on serine/threonine/tyrosine in bacterial signaling and regulation, but very few exact phosphorylation sites have been experimentally determined. Recently, gel‐free high accuracy MS studies reported over 150 phosphorylation sites in two bacterial model organisms Bacillus subtilis and Escherichia coli. Interestingly, the analysis of these phosphorylation sites revealed that most of them are not characteristic for eukaryotic‐type protein kinases, which explains the poor performance of eukaryotic data‐trained phosphorylation predictors on bacterial systems. We used these large bacterial datasets and neural network algorithms to create the first bacteria‐specific protein phosphorylation predictor: NetPhosBac. With respect to predicting bacterial phosphorylation sites, NetPhosBac significantly outperformed all benchmark predictors. Moreover, NetPhosBac predictions of phosphorylation sites in E. coli proteins were experimentally verified on protein and site‐specific levels. In conclusion, NetPhosBac clearly illustrates the advantage of taxa‐specific predictors and we hope it will provide a useful asset to the microbiological community.
Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense
Authors: Widjaja Ivy , Naumann Kai , Roth Udo , Wolf Noreen , Mackey David , Dangl Jeffery L. , Scheel Dierk , Lee Justin 
Published: December 2008

AbstractTransgenic Arabidopsis conditionally expressing the bacterial avrRpm1 type III effector under the control of a dexamethasone‐responsive promoter were used for proteomics studies. This model system permits study of an individual effector without interference from additional bacterial components. Coupling of different prefractionation approaches to high resolution 2‐DE facilitated the discovery of low abundance proteins – enabling the identification of proteins that have escaped detection in similar experiments. A total of 34 differentially regulated protein spots were identified. Four of these (a remorin, a protein phosphatase 2C (PP2C), an RNA‐binding protein, and a C2‐domain‐containing protein) are potentially early signaling components in the interaction between AvrRpm1 and the cognate disease resistance gene product, resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). For the remorin and RNA‐binding protein, involvement of PTM and post‐transcriptional regulation are implicated, respectively.