bluuebunny/crossref_metadata_2025 huggingface dataset:
The next generation of DNA profiling – STR typing by multiplexed PCR – ion‐pair RP LC–ESI time‐of‐flight MS
Authors: Pitterl Florian , Niederstätter Harald , Huber Gabriela , Zimmermann Bettina , Oberacher Herbert , Parson Walther
Published: December 2008

For the first time a multiplexed PCR approach suitable for mass spectrometric STR allele identification is presented. Thirteen forensically important STR markers (vWA, D21S11, D3S1358, D16S539, D8S1179, D7S820, D13S317, D5S818, TPOX, CSF1PO, D2S441, D10S1248, and D22S1045) and the gender typing locus amelogenin were simultaneously amplified. Ion‐pair reversed‐phase high‐performance liquid chromatography electrospray‐ionization time‐of‐flight mass spectrometry (ICEMS) was applied for genotyping, and allowed for highly efficient characterization of multiple PCR amplicons. Compared with electrophoretic sizing ICEMS enabled for the simultaneous detection of length and nucleotide variations. Thus, the obtained amount of biological information present within STR profiles was significantly increased even though the compatibility of typing results with electrophoretically generated data(bases) was maintained. Other advantages of the ICEMS platform included the abandonment of internal size standards, allelic ladders, and any kind of spectral calibration. The 14‐plex PCR was tailor‐made for ICEMS analysis by designing primer pairs that bind close to the repeat region, by using a proof reading polymerase for amplification, and by implementing molecular mass modifiers for prevention of molecular mass overlaps. In a series of experiments, the performance of the multiplexed PCR‐ICEMS assay was evaluated. The ICEMS‐based DNA profiling assay was found to be competitive regarding detection sensitivity and analyzability of degraded and casework samples with commercially available electrophoretic typing approaches, which suggests that multiplexed PCR‐ICEMS assays could represent a valuable tool for (forensic) genetics.
Nanostructured copolymer gels for dsDNA separation by CE
Authors: Wan Fen , Zhang Jun , Lau Angela , Tan Sarah , Burger Christian , Chu Benjamin
Published: December 2008

Pluronics are triblock copolymers of poly(ethylene oxide)‐poly(propylene oxide)‐poly(ethylene oxide) that are able to form many different ordered nanostructures at appropriate polymer concentrations and temperatures in selective solvents. These nanostructured “gels” showed desirable criteria when used as DNA separation media, especially in microchip electrophoresis, including dynamic coating and viscosity switching. A ternary system of F127 (E99P69E99)/TBE buffer/1‐butanol was selected as a model system to test the sieving performance of different nanostructures in separating dsDNA by CE. The nanostructures and their lattice constants were determined by small‐angle X‐ray scattering. Viscosity measurements showed the sol–gel transition phenomena. In addition to the cubic structure, successful electrophoretic separation of dsDNA in 2‐D hexagonally packed cylinders was achieved. Results showed that without further optimization, ΦX174 DNA–Hae III digest was well separated within 15 min in a 7‐cm separation channel, by using F127/TBE/1‐butanol gel with a 2‐D hexagonal structure. A mechanism for DNA separations by those gels with both hydrophilic and hydrophobic domains is discussed.
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

Inbred 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

In 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

Previous 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

A 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

Approximate 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

We 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

DEAD‐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

In 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

A 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

A 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

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

This 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

The 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

The 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

There 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

Transgenic 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.
A dual fluorescent/MALDI chip platform for analyzing enzymatic activity and for protein profiling
Authors: Halim Vincentius A. , Muck Alexander , Hartl Markus , Ibáñez Alfredo J. , Giri Ashok , Erfurth Florian , Baldwin Ian T. , Svatoš Aleš
Published: December 2008

Being able to rapidly and sensitively detect specific enzymatic products is important when screening biological samples for enzymatic activity. We present a simple method for assaying protease activity in the presence of protease inhibitors (PIs) by measuring tryptic peptide accumulation on copolymer pMALDI target chips using a dual fluorescence/MALDI‐TOF‐MS read‐out. The small platform of the chip accommodates microliter amounts of sample and allows for rapid protein digestion. Fluorescamine labeling of tryptic peptides is used to indicate the proteolytic activity and is shown to be an affordable, simple process, yielding a strong fluorescence signal with a low background. Subsequent MALDI‐TOF‐MS analysis, performed in the same sample well, or in a parallel well without adding fluorescamine, detects the specific tryptic peptides and provides confidence in the assay. The dual read‐out method was applied to screen the inhibition activity of plant PIs, components of plant defense against herbivores and pathogens. Extracts of PIs from Solanum nigrum and trypsin were applied together to a pMALDI chip on which a suitable substrate was adsorbed. The fluorescence and MALDI‐TOF‐MS signal decrease were associated with the inhibitory effect of the PIs on trypsin. The developed platform can be modified to screen novel protease inhibitors, namely, those potentially useful for treating or preventing infection by viruses, including HIV and hepatitis C.
British Association for Psychopharmacology Servier satellite meeting: Sleep disturbance
Authors: Chaplin Steve
Published: December 2008

The issue of sleep disturbance, its association with depression and implications for treatment were discussed at a Servier satellite symposium at the Summer meeting of the
British Association for Psychopharmacology in Harrogate. Medical writer Steve Chaplin reports. Copyright © 2008 Wiley Interface Ltd
Photochromism of dihydroindolizines part X. Photo‐responsive self‐assembling organogelators based on photochromic dihydroindolizines and 11‐aminoundecanoic acid (AUDA)
Authors: Ahmed Saleh A. , Moussa Ziad , Al‐Raqa Shaya Y. , Alamry Saleh N.
Published: December 2008

Multi‐addressable photophysical properties of new synthesized photochromic materials based on photochromic dihydroindolizine system (DHI) covalently linked to N‐acyl‐11 aminoundecanoic acid (AUDA) or to its sodium salt or to its ester, through an amidic or urethane linkage have been studied. The DHI skeleton in these compounds is substituted in both the fluorene part (region A) or in the heterocyclic base (region B) with the gelling moieties. These molecules have been designed to respond to their environment. Interestingly, they are shown to act as efficient gelators for polar organic fluids, water and obviously they exhibit a thermosensitive answer as low molecular mass organogelators. In these fluids, the aggregative properties are totally suppressed upon conversion to neutral carboxylic species. The gels of these carboxylate sodium salts are shown to be markedly affected by light irradiation. Supramolecular gelating assemblies can be disrupted by the photoinduced ring opening of the DHI subunit, so that the macroscopic flowing property is recovered. Upon a further thermal treatment, the system is reversibly converted back to the supramolecular network. Controlled gelation could be achieved using temperature, light, or acidity as external stimuli. These new synthesized photochromic gels with their multi‐addressable properties will find their applications as super photoresponsive materials. Developing and tuning of the photophysical properties of the synthesized compounds by the amide and urethane substituents in the 4‐position of the fluorene and pyridazine regions have been achieved. The absorption maxima (λmax) and the half‐lives (t1/2) of the colored betaines were detected in all cases using UV/VIS spectrophotometric measurements. Irradiation of DHI 12‐20 in CH2Cl2 or in acetonitrile solutions at ambient temperature with polychromatic light leads to the formation of red to red‐violet colored betaines 12′‐20′. The kinetics of the bleaching process of betaines 12′‐20′ to DHIs 12‐20 were found to take place in the second range (96‐218 s) and fit well the first order thermal back reaction. Some of these DHIs showed a photostability higher than that of the standard one. These interesting photophysical properties will help this family of compounds to find useful applications. Copyright © 2008 John Wiley & Sons, Ltd.
Density functional and spectroscopic studies of nitrogen inversion in substituted dizocilpines
Authors: Aliev Abil E. , Sinclair Alex J. , Zhou Shen , Wilden John D. , Caddick Stephen , Kullmann Dimitri M. , Rusakov Dmitri A.
Published: December 2008

While developing a synthesis towards tagged dizocilpine (MK‐801) analogues, we observed highly restricted inversion of a nitrogen centre in a number hydroxylamines obtained as key intermediates. These compounds are shown to possess some of the structural elements which are expected to significantly hinder the nitrogen inversion, potentially leading to hydroxylamines with a chiral nitrogen centre. Free energy barriers (ΔG≠) of the nitrogen inversion were estimated to be ca. 22 kcal mol−1 at temperatures near 420 K using variable temperature NMR measurements in DMSO‐d6. Further density functional studies of a number model systems were undertaken in order to better rationalize the measured inversion barriers and follow the role of various structural factors in raising the barrier height of the nitrogen inversion process. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitative structure–reactivity relationship studies on the catalyzed Michael addition reactions
Authors: Hemmateenejad Bahram , Sanchooli Mahmood , Mehdipour Ahmadreza
Published: December 2008

Quantitative structure–reactivity relationship (QSRR) can be considered as a variant of quantitative structure–property relationship (QSPR) studies, where the chemical reactivity of reactants or catalysts in a specified chemical reaction is related to chemical structure. In this manner, the Michael addition of some different substrates using different catalysts (SDS, silica gel, and ZrOCl2) was subjected to structure–reactivity relationship, quantitatively. Multiple linear regression (MLR) and partial least square (PLS) were used to perform the QSRR analysis. The resulted models for different catalyzed reactions showed that the catalysts probably act in different mechanisms since the models obtained for the catalysts included different parameters from substrate and enones. Overall, it was found that the reactivity in Michael addition reactions is controlled by coulombic (dipole and charge) interactions as well as the orbital energetic parameters. In the presence of different catalysts, the relative importance of these parameters is changed and hence the catalytic activity is changed. Copyright © 2008 John Wiley & Sons, Ltd.
In vitrometabolism ofβ‐lapachone (ARQ 501) in mammalian hepatocytes and cultured human cells
Authors: Miao Xiu‐Sheng , Zhong Caiyun , Wang Yunxia , Savage Ronald E. , Yang Rui‐Yang , Kizer Darin , Volckova Erika , Ashwell Mark A. , Chan Thomas C. K.
Published: December 2008

ARQ 501 (3,4‐dihydro‐2,2‐dimethyl‐2H‐naphthol[1,2‐b]pyran‐5,6‐dione,β‐lapachone) is an anticancer agent, currently in multiple phase II clinical trials as monotherapy and in combination with other cytotoxic drugs. This study focuses onin vitrometabolism in cryopreserved hepatocytes from mice, rats, dogs and humans using [14C]‐labeled ARQ 501. Metabolite profiles were characterized using liquid chromatography/mass spectrometry combined with an accurate radioactivity counter. Ion trap mass spectrometry was employed for further structural elucidation. A total of twelve metabolites were detected in the mammalian hepatocytes studied; all of which but one were generated from phase II conjugation reactions. Ten of the observed metabolites were produced by conjugations occurring at the reducedortho‐quinone carbonyl groups of ARQ 501. The metabolite profiles revealed that glucuronidation was the major biotransformation pathway in mouse and human hepatocytes. Monosulfation was the major pathway in dog, while, in rat, it appears glucuronidation and sulfation pathways contributed equally. Three major metabolites were found in rats: monoglucuronide M1, monosulfate M6, and glucuronide‐sulfate M9. Two types of diconjugation metabolites were formed by attachment of the second glycone to an adjacent hydroxyl or to an existing glycone. Of the diconjugation metabolites, glucosylsulfate M10, diglucuronide M5, and glucuronide‐glucoside M11 represent rarely observed phase II metabolites in mammals. The only unconjugated metabolite was generated through hydrolysis and was observed in rat, dog and human hepatocytes. ARQ 501 appeared less stable in human hepatocytes than in those of other species. To further elucidate the metabolism of ARQ 501 in extrahepatic sites, its metabolism in human kidney, lung and intestine cells was also studied, and only monoglucuronide M1 was observed in all the cell types examined. Copyright © 2008 John Wiley & Sons, Ltd.
Liquid chromatography/negative ion atmospheric pressure photoionization mass spectrometry: a highly sensitive method for the analysis of organic explosives
Authors: Song Liguo , Bartmess John E.
Published: December 2008

Gas chromatography/mass spectrometry (GC/MS) is applied to the analysis of volatile and thermally stable compounds, while liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (LC/APCI‐MS) and liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) are preferred for the analysis of compounds with solution acid‐base chemistry. Because organic explosives are compounds with low polarity and some of them are thermally labile, they have not been very well analyzed by GC/MS, LC/APCI‐MS and LC/ESI‐MS. Herein, we demonstrate liquid chromatography/negative ion atmospheric pressure photoionization mass spectrometry (LC/NI‐APPI‐MS) as a novel and highly sensitive method for their analysis. Using LC/NI‐APPI‐MS, limits of quantification (LOQs) of nitroaromatics and nitramines down to the middle pg range have been achieved in full MS scan mode, which are approximately one order to two orders magnitude lower than those previously reported using GC/MS or LC/APCI‐MS. The calibration dynamic ranges achieved by LC/NI‐APPI‐MS are also wider than those using GC/MS and LC/APCI‐MS. The reproducibility of LC/NI‐APPI‐MS is also very reliable, with the intraday and interday variabilities by coefficient of variation (CV) of 0.2–3.4% and 0.6–1.9% for 2,4,6‐trinitrotoluene (2,4,6‐TNT). Copyright © 2008 John Wiley & Sons, Ltd.
Reliability‐based performance‐based design: learning from Allin Cornell
Authors: Skokan Matthew J. , Hart Gary C.
Published: December 2008

This paper presents a restatement, clarification and expansion of one aspect of the published work on the topic of performance based design of Professor Allin Cornell. Copyright © 2008 John Wiley & Sons, Ltd.
Is Carotid Endarterectomy a Trainee Operation?
Authors: Lutz Hans‐Joachim , Michael R. , Gahl B. , Savolainen H.
Published: December 2008

Background

Recent dramatic changes in surgical training resulting from working‐hour regulations may lead to lack of competence. Traditionally, carotid surgery has been the domain of specialists. This study was designed to compare the outcome of carotid endarterectomy performed by vascular surgical trainees versus vascular surgeon (VS).

Methods

A retrospective study of 1,379 consecutive patients who underwent carotid endarterectomy as the sole procedure under local or general anesthesia (from 1995–2004) was performed. All patients were admitted to the intensive care unit for 24 hours. Trainees performed 475 (34.5%) and vascular specialists performed 904 (65.5%) operations.

Results

Patient characteristics with regard to preoperative neurological status were similar. Trainees operated on 61.4% symptomatic patients and VS on 56.8% (P = 0.09). Shunt use did not differ (16% trainee vs. 17.8% VS). Clamping time and total operating time were longer among trainees (41.9 vs. 33.5 min, P < 0.001; and 121.2 vs. 101.8 min, P < 0.001, respectively). Postoperative stroke and death rates (3.2% vs. 3.1% and 0.4% vs. 0.9%, respectively) did not differ. Peripheral nerve complications were more common among trainees (12.2% vs. 6.5%; P < 0.0001); 99.6% of these nerve injuries had resolved at 3 months’ follow‐up.

Conclusions

Carotid endarterectomy can be performed safely by a trainee vascular surgeon when assisted and supervised by a specialist vascular surgeon.
Current Understanding and Potential Immunotherapy for HIV‐Associated Squamous Cell Carcinoma of the Anus (SCCA)
Authors: Marin‐Muller Christian , Li Min , Chen Changyi , Yao Qizhi
Published: December 2008

Squamous cell carcinoma of the anus (SCCA) is a rare disease in the average population but is an increasing concern among immunocompromised individuals, such as the HIV‐seropositive. Coinfection with human papillomavirus (HPV) in this population is common. HPV infection is difficult to clear with a compromised immune system, which results in a greater risk of tumor development and a more aggressive progression of the disease. The recent approval of a prophylactic HPV vaccine for cervical cancer has sparked an interest in a search for improved immunotherapeutic multimodality therapies to combat anogenital tumors associated with the virus. In this review, we discuss the known mechanisms of action of HIV‐associated SCCA, examine the current treatments for the disease, and focus on the potential of an immunotherapeutic vaccine approach for both prophylactic and therapeutic application.
Persistent Posterior Interosseous Nerve Palsy Associated with a Chronic Type I Monteggia Fracture-Dislocation in a Child: A Case Report and Review of the Literature
Authors: Ruchelsman David E. , Pasqualetto Michele , Price Andrew E. , Grossman John A. I.
Published: December 2008

We present a rare case of persistent complete posterior interosseous nerve palsy associated with a chronic type I Monteggia elbow fracture-dislocation consisting of anterior dislocation of the radial head and malunion of the ulna in an 8-year-old child requiring surgical treatment. Posterior interosseous nerve neuropraxia following acute Monteggia injury patterns about the elbow has been described and is thought to be secondary to traction or direct trauma. The condition typically resolves following successful closed reduction of the radial head. This report describes combined treatment of the nerve and skeletal injury for the chronic type I Monteggia injury. The literature is reviewed, and diagnostic challenges with and treatment options for chronic Monteggia fracture-dislocations in children are discussed.
Linear Rashba Model of a Hydrogenic Donor Impurity in GaAs/GaAlAs Quantum Wells
Authors: Li Shu-Shen , Xia Jian-Bai
Published: December 2008

The Rashba spin-orbit splitting of a hydrogenic donor impurity in GaAs/GaAlAs quantum wells is investigated theoretically in the framework of effective-mass envelope function theory. The Rashba effect near the interface between GaAs and GaAlAs is assumed to be a linear relation with the distance from the quantum well side. We find that the splitting energy of the excited state is larger and less dependent on the position of the impurity than that of the ground state. Our results are useful for the application of Rashba spin-orbit coupling to photoelectric devices.
A Rapid Synthesis of Oriented Palladium Nanoparticles by UV Irradiation
Authors: Navaladian S , Viswanathan B , Varadarajan TK , Viswanath RP
Published: December 2008

Palladium nanoparticles of average size around 8 nm have been synthesized rapidly by UV irradiation of mixture of palladium chloride and potassium oxalate solutions. A rod-shaped palladium oxalate complex has been observed as an intermediate. In the absence of potassium oxalate, no Pd nanoparticles have been observed. The synthesized Pd nanoparticles have been characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), selective area electron diffraction and energy dispersive analysis by X-rays (EDAX) analyses. XRD analysis indicates the preferential orientation of catalytically active {111} planes in Pd nanoparticles. A plausible mechanism has been proposed for the formation of anisotropic Pd nanoparticles.
Fatty Acid Biomarkers of Symbionts and Unusual Inhibition of Tetracosapolyenoic Acid Biosynthesis in Corals (Octocorallia)
Authors: Imbs Andrey B. , Demidkova Darya A. , Dautova Tatyana N. , Latyshev Nikolay A.
Published: December 2008

Seven zooxanthellae‐free species of octocorals (the genera Acanthogorgia, Acabaria, Chironephthya, Echinogorgia, Menella, Ellisella, and Bebryce) and two zooxanthellate octocorals (the genera Paralemnalia and Rumphella) were examined to elucidate their fatty acid (FA) composition. Arachidonic (about 40% of the total FA) and palmitic acids were predominant in all the species studied. Seven furan FA (F‐acids) (up to 9.7%) were identified in the azooxanthellate octocorals. The main F‐acids were 14,17‐epoxy‐15‐methyldocosa‐14,16‐dienoic and 14,17‐epoxy‐15,16‐dimethyldocosa‐14,16‐dienoic acids. In all specimens of Bebryce studeri, C25–28 demospongic FA (about 20%) were identified. These FA reflect the presence of a symbiotic sponge in B. studeri and can be used as the specific markers for other corals. A significant difference (P < 0.01) between azooxanthellate and zooxanthellate corals was found for odd‐chain and methyl‐branched saturated FA, 18:1n‐7, and 7‐Me‐16:1n‐10; that indicated the presence of an advanced bacterial community in azooxanthellate corals. The zooxanthellate species were distinguished by significant amounts of 18:3n‐6, 18:4n‐3, and 16:2n‐7 acids, which are proposed as the markers of zooxanthellae in soft corals. Contrary to the normal level of 24:5n‐6 (9.4%) and 22:4n‐6 (0.6%), unexpected low concentrations of 24:5n‐6 (0.4%) accompanied by a high content of 22:4n‐6 (up to 11.9%) were detected in some specimens. The presence of an unknown factor in octocorals, specific for n‐6 PUFA, which inhibited elongation of 22:4n‐6 to 24:4n‐6, is conjectured.
Optimization of Synthetic Conditions for the Preparation of Dihomo‐γ‐Linolenic Acid from γ‐Linolenic Acid
Authors: Xue Gang , Liu Fengxia , Wang Ying , Huang Kaixun
Published: December 2008

Orthogonal experiments were employed to optimize the correlated parameters of reduction, sulfonation, substitution and hydrolysis. These reactions were used to convert γ‐linolenic acids into dihomo‐γ‐linolenic acids (DGLA). For the reduction, the best reaction conditions were at 35 °C for 4.5 h with LiAlH4 and γ‐linolenic acid (in the ratio of 40 g:100 g); for the sulfonation, reaction at 29 °C for 3.5 h with 150 g γ‐linolenic alcohol and 65 mL mesyl chloride, then the water phase being extracted with dichloromethane (3 × 100 mL); for the substitution, the reaction at 80 °C for 2.5 h with metallic sodium and sulfonate (at a ratio of 8 g:100 g); and for the hydrolysis, reaction at 80 °C for 2.5 h with NaOH and dihomo dioate (at a ratio of 50 g:100 g). The four reactions gave yields that exceeded 90% for each step. Finally, crystallization and decarboxylation provided DGLA in an overall yield of 60% and >95% purity.
Phospholipid Composition of Jatropha curcus Seed Lipids
Authors: Rao Kotte Sagar , Chakrabarti Pradosh Prasad , Rao B. V. S. K. , Prasad R. B. N.
Published: December 2008

Jatropha curcus L. oil has emerged as one of the most important raw materials for biodiesel production. However, no detailed study has been reported on characterizing the lipid constituents of jatropha oil. The present study revealed that the total oil content of jatropha seeds was 32% with a composition of 97.6% neutral lipids, 0.95% glycolipids and 1.45% phospholipids. The fatty acid composition of total lipids, neutral lipids, phospholipids and glycolipids was also determined and found to contain oleic acid (18:1) and linoleic acids (18:2) as major fatty acids. The phospholipids fraction was further characterized and quantified and found to contain phosphatidyl choline (PC) 60.5%, phosphatidyl inositol (PI) 24% and phosphatidyl ethanolamine (PE) 15.5%. The fatty acid composition and the positional distribution of the fatty acids of individual phospholipids were also reported.