bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualization of Thermo‐Oxidative Degradation of Polyolefins in Solution Using HT‐SEC and HT‐AF4‐MALS
Authors: Otte Tino , Pasch Harald , Brüll Robert , Macko Tibor
Published: January 2011

The molar mass distributions of high‐molar‐mass PE and PP were characterized using HT‐AF4 and HT‐SEC in combination with IR and MALS detection. Calculated molar mass distributions, average molar masses and radii of gyration were compared. It was found that HT‐AF4 can detect the real extent of thermo‐oxidative degradation during dissolution. HT‐SEC is affected by shear and thermo‐oxidative degradation while in HT‐AF4 no shear stress exists. As a consequence, the molar mass averages obtained from HT‐SEC are pronouncedly lower as obtained from HT‐AF4. In addition, branched polyolefins cannot be correctly characterized by SEC‐MALS due to abnormal co‐elution effects. HT‐AF4 is therefore the method of choice for studying the thermo‐oxidative degradation of macromolecules with high molar masses.

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Silver Nanoparticles in Blends of Polyethylene and a Superabsorbent Polymer: Morphology and Silver Ion Release
Authors: Stará Hana , Starý Zdeněk , Münstedt Helmut
Published: January 2011

Antimicrobial properties of polymer materials are required in many applications. The polyethylene/superabsorbent polymer (PE/SAP) blends containing silver nanoparticles were successfully prepared via thermal reduction during melt mixing. It was found that in situ formed silver nanoparticles are preferentially located at the interface between PE matrix and SAP particles. The expectation was that the low water uptake of the PE will be enhanced by blending with a SAP and thus the silver ion release from the material will increase. Surprisingly, the silver ion release was markedly suppressed by the addition of SAP. This finding is explained by the preferential sorption of silver ions by the SAP particles.

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Poly(propylene)/Carbon Nanofiber Nanocomposites: Ex Situ Solvent‐Assisted Preparation and Analysis of Electrical and Electronic Properties
Authors: Chen Xuelong , Wei Suying , Yadav Atarsingh , Patil Rahul , Zhu Jiahua , Ximenes Rey , Sun Luyi , Guo Zhanhu
Published: January 2011

CNF‐reinforced PP nanocomposites were fabricated from CNFs dispersed in a boiling PP/xylene solution. Their thermal properties were characterized by TGA and DSC and shown to exhibit improved thermal stability and higher crystallinity. They were further processed into thin films by compression molding. The electrical conductivity and dielectric property of the PP/CNF nanocomposite thin films were studied. Both electric conductivity and real permittivity increased with increasing fiber loading. Electrical conductivity percolation is observed between 3.0 and 5.0 wt.‐% fiber loading. The rheological behavior of the nanocomposite melts were also investigated. It was found that a small fiber concentration affects the modulus and viscosity of PP melt significantly.

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Thermoresponsive Block Copolymer–Protein Conjugates Prepared by Grafting‐from via RAFT Polymerization
Authors: Li Ming , Li Hongmei , De Priyadarsi , Sumerlin Brent S.
Published: January 2011

Well‐defined “smart” block copolymer–protein conjugates were prepared by two consecutive “grafting‐from” reactions via reversible addition–fragmentation chain transfer (RAFT) polymerization. The initiating portion (R‐group) of the RAFT agent was anchored to a model protein such that the thiocarbonylthio moiety was readily accessible for chain transfer with propagating chains in solution. Well‐defined polymer‐protein conjugates of poly(N‐isopropylacrylamide) (PNIPAM) and bovine serum albumin (BSA) were prepared at room temperature in aqueous media. The retained trithiocarbonate moiety on the free end group of the immobilized polymer allowed the homopolymer conjugate to be extended by polymerization of N,N‐dimethylacrylamide. Polyacrylamide gel electrophoresis, size exclusion chromatography, and NMR spectroscopy confirmed the synthesis of the various conjugates and revealed that the polymerizations were well controlled. As expected, the resulting block copolymer–protein conjugates demonstrated thermoresponsive behavior due to the temperature‐sensitivity of the PNIPAM block, as evidenced by turbidity measurements and dynamic light scattering analysis.

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Cyclodextrin Supramacromolecules: Unexpected Formation in Aqueous Phase under Ambient Conditions
Authors: Rao J. P. , Geckeler Kurt E.
Published: January 2011

The unexpected formation of supramacromolecules of β‐cyclodextrin in aqueous solution under ambient conditions is reported in this article. The shape and size of the supramacromolecules could be controlled by varying the stirring time and the concentration. The supramolecular interactions of the supramacromolecules were confirmed by 1H NMR spectroscopy. Additionally, visual evidence of the supramacromolecules was provided by transmission and scanning electron microscopy. The thermal behavior of the supramacromolecules was examined by thermogravimetric analysis. The molecular mass determination by gel permeation chromatography showed that the supramacromolecules had a high molar mass.

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A Novel Low Solvent Method for Grafting Polyaniline to Silylated Silica
Authors: Wheelwright Walt V.K. , Ray Sudip , Easteal Allan J.
Published: January 2011

Summary: Silica gel, an important inorganic polymer with many applications, was silylated with 3‐(phenylaminopropyl)trimethoxysilane (PAPTMOS) by means of a novel “low solvent” method, whereby the silane was dissolved in a small amount of methanol, mixed with silica and reaction carried out in a heated vacuum oven. Polyaniline (PANI) was grafted to the silylated silica by in situ polymerization of aniline, then dedoped with aqueous ammonia. Physically adsorbed PANI was removed from the modified silica by washing with tetrahydrofuran (THF) and N‐methyl‐2‐pyrrolidone (NMP). The silylated, PANI‐modified silica had electrical conductivity 1.2 × 10−3 S cm−1 after being re‐doped with methanesulfonic acid. FTIR, elemental analysis, X‐ray photoelectron spectroscopy, solid‐state 13C and 29Si NMR and morphological studies by SEM confirmed successful formation of the SiO2‐polyaniline hybrid material.
Effect of two Kinds of Imidazolium Ionic Liquids on the Microemulsion Polymerization of Methyl methylacrylate
Authors: Lu Jingjing , Ding Yunsheng , Yu Yun , Wu Shuying , Feng Wanggao
Published: January 2011

Summary: In this paper, the microemulsion polymerization of methyl methylacrylate (MMA) was carried out with single and gemini ionic liquids as emulsifier including 1‐N‐tetradecyl‐3‐methylimidazolium bromide (C14MIM · Br) and 1, 4‐Bis (3‐tetradecylimidazolium‐1‐yl) butane bromide (C14MIM‐4‐C14MIM · 2Br) respectively, and they were all have typical microemulsion polymerization characters of MMA, but the process of polymerization directly depends on the structure of the imidazolium ionic liquids. The structure and concentration of ionic liquids have effects on the resulted latex particle sizes of PMMA, and much smaller size latexes of PMMA could be gotten with C14MIM · Br as emulsifier than C14MIM‐4‐C14MIM · 2Br in polymerization. On the other hand, the structure of emulsifier has the effects on the molecular weight (MW) and molecular weight distribution (MWD) of PMMA, so the resulting PMMA prepared from microemulsion polymerization with C14MIM · Br as emulsifier has higher MW but narrower MWD than that of PMMA with the same dosage of C14MIM‐4‐C14MIM · 2Br as emulsifier.
Preparation and Barrier Properties of Chitosan‐Layered Silicate Nanocomposite Films
Authors: Oguzlu Hale , Tihminlioglu Funda
Published: January 2011

Summary: In this study, chitosan nanocomposite films were prepared using a solvent‐casting method by incorporation of an organically modified montmorillonite (Cloisite 10A). The effect of filler concentration on the water vapor permeability, oxygen permeability, mechanical and thermal properties of the composite films was evaluated. The structure of nanocomposites and the state of intercalation of the clay were characterized by XRD. The water vapor permeability of pure chitosan films was measured as a function of relative humidity (RH). It was found that the permeability value increased with an increase in RH. The water vapor and gas permeability values of the composite films decreased significantly with increasing filler concentration. Permeation data was fitted to various phenomenological models predicting the permeability of polymer systems filled with nanoclays as a function of clay concentration and aspect ratio of nanoplatelets. According to the XRD results, an increase in basal spacing was obtained with respect to pure clay for chitosan/clay nanocomposites. This demonstrated the formation of intercalated structure of clay in the polymer matrix. Tensile strength and elongation at break of the composites increased significantly with the addition of clay, however the thermal and color properties of the films were not much affected by the intercalation of clay into polymer matrix.
Preparation and Characterization of In‐Situ Polymerized Nanocomposites Based on Polyaniline in Presence of MWCNTs
Authors: Moniruzzaman Md. , Das C. K.
Published: January 2011

Summary: Polyaniline (PANI) composites were prepared with both unmodified and amine modified MWCNTs with and without BaTiO3 through in‐situ oxidative polymerization. Uniform coating of PANI on the MWCNTs and BaTiO3 surfaces was found which was evident from the Field Emission Scanning Electron Microscopic (FESEM) and High Resolution Transmission Electron Microscopic (HRTEM) images. The structure of pure and amine modified MWCNTs was identified by Fourier Transform Infrared Spectroscopy (FTIR). The thermal stability of the amine modified composite with BaTiO3 is higher than that of the unmodified composite because of the better affinity between modified MWCNTs and polymer matrix and due to the higher stability of barium titanate itself. The capacitance of amine modified MWCNTs and BaTiO3 composites was less than that of the pure MWCNTs composites but the thermal stability increased in amine modified MWCNTs and BaTiO3 composites with respect to the pure MWCNTs composites. The maximum capacitance and energy density values were found in MWCNT/PANI composites which were equal to 523.20 F/g and 142.83 Wh/kg respectively at a scan rate of 10mv/s. Maximum power density was found to be 5147.70 W/kg in the same composite at a scan rate of 200 mv/s.
Implementation of Specific Bioconjugation in Polystyrene‐block‐poly(tert‐butyl acrylate)‐Based Bio‐Interfaces
Authors: Wasse1 Ekram , Ghassemi Sina , Schönherr Holger
Published: January 2011

Summary: Here we report on the expansion of a previously introduced biointerface platform based on thin spin‐coated films of polystyrene‐block‐poly(tert‐butyl acrylate) (PS‐b‐PtBA). Following the selective deprotection of the tert‐butyl‐ester groups in the PtBA skin layer by hydrolysis under acidic conditions, the activation with N‐hydroxysuccinimide and the subsequent derivatization with α,ω‐biotin‐amine end‐functionalized poly(ethylene glycol) (PEG), strepavidin was immobilized as anchor layer for specific immobilization of biotin‐tagged molecules. Based on contact angle, Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM) and confocal fluorescence microscopy data it was shown that the polymer films were efficiently modified. The complexation of a biotin‐tagged dye, as well as the non‐specific adsorption of proteins was determined by confocal fluorescence microscopy measurements. The surface coverage of the immobilized dye as a function of dye concentration in solution was found to be consistent with a high affinity‐type adsorption isotherm, while the protein resistant properties were found to be similar to non‐biotinylated PEG. The scope of micro‐ and nanostructured PS‐b‐PtBA biointerfaces is thereby considerably expanded to encompass the specific immobilization of biotin‐tagged biomolecules.
Characterization of Ethylene methyl methacrylate and Ethylene butylacrylate Copolymers with Interactive Liquid Chromatography
Authors: Chitta Rajesh , Brüll Robert , Macko Tibor , Monteil Vincent , Boisson Christophe , Grau Etienne , Leblanc Alexandra
Published: January 2011

Summary: Copolymers of ethylene with methyl methacrylate (EMMA) and butyl acrylate (EBA), which are of different average chemical composition and block lengths according to NMR analysis, were analyzed by size exclusion chromatography (SEC), differential scanning calorimetry (DSC), Crystallization Analysis Fractionation (CRYSTAF), and high performance liquid chromatography at high temperature (HT‐HPLC). With CRYSTAF and DSC crystallizing fractions were detected only in some samples. HT‐HPLC fractionated all the samples irrespective of their crystallinity. Homopolymers, PMMA and PE were also found in the copolymer samples of EMMA. EMMA and EBA were separated in HPLC according to the content of polar comonomer. A linear correlation between the MMA content and elution volume could not be established due to the presence of homopolymers as admixtures. In such a case the average chemical composition obtained by NMR does not correspond to the real chemical composition of the copolymers. Unlike EMMA the EBA samples eluted in single peaks, which was used for evaluation of their chemical composition distribution. The comparison of results obtained by fractionation via CRYSTAF and HT‐HPLC clearly demonstrates the advantages of the chromatographic approach to study the chemical heterogeneity of olefin based copolymers.
Synthesis and Characterization of Hexathiophenes with Methylthienyl Side Chains
Authors: Saini Geeta , Jacob Josemon
Published: January 2011

Summary: Two novel conjugated isomeric hexathiophenes 6T1 and 6T2 bearing 5‐methyl‐2‐thienyl substituents have been synthesized by Suzuki coupling and oxidative dimerization method. These isomers were characterized by 1H NMR, 13C NMR, elemental and mass analysis. The two hexamers show good solubility in common solvents and show almost identical UV‐vis absorption spectra in solution with a maximum cantered at 387 nm. These materials bearing thienyl substituents in the sidechain are anticipated to provide better charge transport in devices and hold promise for use in organic field effect transistors.
The british clearing banks and north sea financing
Authors: Baird R. G.
Published: January 2011

This article reviews available data on North Sea financing with respect to the provision of funds for the offshore exploration and development effort of the oil companies, and for the onshore components suppliers and service companies. In particular it examines the role of the British clearing banks and the changes induced in their lending techniques and habits by the demands of the oil industry. It concludes that financial provision has been adequate and that neither the pace of oil development nor the participation of British industry in the offshore markets has suffered for lack of ready funding.
An analysis of the economic impact of north sea oil activity on the scottish economy in 1973
Authors: Al‐Ali H. M. , Burdekin R.
Published: January 2011

There was no production of crude oil and natural gas in 1973. However, exploration and preparatory production work were well underway. The paper examines the impact within Scotland in 1973 of the expenditure required to supply these activities. The data used for the study are those contained in or associated with the 1973 Scottish Input Output tables and the analysis uses input‐output techniques. The pattern of crude oil consumption within the Scottish economy in 1973 is also examined.
The role of entry barriers in the development of the offshore supply sector in scotland
Authors: Moar Lyle
Published: January 2011

This paper examines the offshore oil supply sector and shows how the entry barriers experienced by new supply firms are imposed not by other supply firms but by the oil companies. This is done to ensure product quality and reliability of service rather than the more general attention to price considerations. The range of entry barriers are discussed in relation to key characteristics of the oil industry. As a spin‐off this experience appears to have generated a more responsive attitude towards technological and commercial change throughout Scottish industry.
The impact of oil on the shetland economy
Authors: McNicoll I. H.
Published: January 2011

This paper uses input‐output analysis to measure the impact of oil supply bases and oil construction on the economy of Shetland. The output, income and employment created in each local industry by oil activities is measured. Oil industry multipliers are derived. Possible negative effects of oil on the local economy are considered. Finally, a forecast is made of the impact of oil on the Shetland economy in 1985.
Why should firms manufacture retailer brands?
Authors: Morris David , Nightingale John
Published: January 2011

For firms manufacturing convenience goods there are three branding policies available, a proprietory brand policy, a retailer brand policy and a mixed brand policy. A firm's choice depends on differences in demand and promotion costs between the proprietory and retailer brand markets. This can be analysed using a simple elaboration of the standard 3rd degree price discrimination model. But if the two markets are not independent over the long‐term there may be other consequences of following the optimization rules of the model. If retailers develop consumers' preference for their own shops and their own brands, the demand advantage enjoyed by manufacturers' brands may be reduced further. The more willing are manufacturers to supply retailer brands, the more retailers win undermine the demand for manufacturers' proprietory brands.
Foreign capital inflows, domestic savings and the price of political stability in the sudan: Weisskopf revisited
Authors: Henley John S. , Droucopoulos Vassilis , Ibrahim Mohamed A.
Published: January 2011

This paper reworks Weisskopf's estimates of the effect of foreign capital inflow on domestic savings for a later time period. The Sudan is presented as an example of a public sector dominated economy, dependent on one major export crop and politically unstable. While Weisskopf's savings function had an indication of a negative relationship between public sector savings and official foreign capital inflow, problems of collinearity between the independent variables cast doubt on its utility for analysis of economies dependent on limited primary exports. The negative relationship between public sector savings and official is explained in terms of the expansion of the state's bureaucracy and military.
Share‐ownership schemes for employees – proposals and prospects
Authors: White P. J.
Published: January 2011

Recent statutory and other developments in the United Kingdom seem to have stimulated the introduction of share‐ownership schemes for employees. This article considers the merits of such schemes, and their potential role within companies. The article also points up some weaknesses in the 1978 Finance Act, and suggests the need for caution on the part of those in industry who might contemplate the introduction of share‐ownership arrangements.
Identification of glucosinolate congeners able to form DNA adducts and to induce mutations upon activation by myrosinase
Authors: Baasanjav‐Gerber Chimgee , Monien Bernhard Hans , Mewis Inga , Schreiner Monika , Barillari Jessica , Iori Renato , Glatt Hansruedi
Published: January 2011

Scope: Juices from Brassicales are mutagenic in Salmonella typhimurium and characteristic adducts are formed with the endogenous DNA in Brassicales homogenates. These effects require myrosinase activity, suggesting an involvement of breakdown products of glucosinolates (GLs). We aimed to identify GLs congeners producing these effects.

Methods and results: We investigated twelve individual GLs for mutagenicity in S. typhimurium TA104 and TA100 and for adduct formation with herring sperm DNA using the 32P‐postlabelling/thin‐layer chromatography method. All bacteriotoxic and mutagenic effects observed required the presence of myrosinase. Neoglucobrassicin, 4‐methoxyglucobrassicin and sinalbin showed mutagenicity over wide concentration ranges, with neoglucobrassicin being the most potent congener. Six other GLs led to modest increases in the number of revertants in a small concentration range, before toxicity overshadowed this effect. The remaining three GLs showed some toxicity, but no mutagenicity. However, all twelve GLs formed DNA adducts. Clearly the highest adduct levels were detected with the indole GLs tested. They matched the major adduct spots formed in Brassicales homogenates.

Conclusion: The observation that GLs are genotoxic demands follow‐up studies on possible genotoxic and carcinogenic effects of these common food compounds in animal models and humans. Our study may be used to prioritize the congeners in further studies.
Redox‐sensitive proteome and antioxidant strategies in wheat seed dormancy control
Authors: Bykova Natalia V. , Hoehn Brenda , Rampitsch Christof , Banks Travis , Stebbing Jo‐Ann , Fan Tao , Knox Ron
Published: January 2011

Oxidative signalling by ROS has been demonstrated to play a role in seed dormancy alleviation, but the detailed molecular mechanisms underlying this process remain largely unknown. Here, we show dynamic differences in redox‐sensitive proteome upon wheat seed dormancy release. Using thiol‐specific fluorescent labelling, solubility‐based protein fractionation, 2‐D IEF PAGE, and MS analysis in conjunction with wheat EST sequence libraries, proteins with reversible oxidoreductive changes were characterized. Altogether, 193 reactive Cys were found in 79 unique proteins responding differentially in dormant, non‐dormant, abscisic, or gibberellic acid‐treated seed protein extracts from RL4137, a wheat cultivar with extreme dormancy. The identified proteins included groups that are redox‐, stress‐, and pathogen‐responsive, involved in protein synthesis and storage, are enzymes of carbohydrate metabolism, proteases, and those involved in transport and signal transduction. Two types of redox response could be detected: (i) a dramatic increase in protein thiol redox state in seeds during imbibition and hormonal treatment; (ii) higher antioxidant capacity related to sensing of a threshold redox potential and balancing the existing redox pools, in dry dormant versus non‐dormant seeds. These results highlight occurrence of the antioxidant defence mechanisms required for the protection of seed during a dormancy stage.
Tyrosine 656 in topoisomerase IIβ is important for the catalytic activity of the enzyme: Identification based on artifactual +80‐Da modification at this site
Authors: Grozav Adrian G. , Willard Belinda B. , Kozuki Toshiyuki , Chikamori Kenichi , Micluta Marius A. , Petrescu Andrei‐Jose , Kinter Michael , Ganapathi Ram , Ganapathi Mahrukh K.
Published: January 2011

Topoisomerase (topo) II catalyzes topological changes in DNA. Although both human isozymes, topo IIα and β are phosphorylated, site‐specific phosphorylation of topo IIβ is poorly characterized. Using LC‐MS/MS analysis of topo IIβ, cleaved with trypsin, Arg C or cyanogen bromide (CNBr) plus trypsin, we detected four +80‐Da modified sites: tyr656, ser1395, thr1426 and ser1545. Phosphorylation at ser1395, thr1426 and ser1545 was established based on neutral loss of H3PO4 (−98 Da) in the CID spectra and on differences in 2‐D‐phosphopeptide maps of 32P‐labeled wild‐type (WT) and S1395A or T1426A/S1545A mutant topo IIβ. However, phosphorylation at tyr656 could not be verified by 2‐D‐phosphopeptide mapping of 32P‐labeled WT and Y656F mutant protein or by Western blotting with phosphotyrosine‐specific antibodies. Since the +80‐Da modification on tyr656 was observed exclusively during cleavage with CNBr and trypsin, this modification likely represented bromination, which occurred during CNBr cleavage. Re‐evaluation of the CID spectra identified +78/+80‐Da fragment ions in CID spectra of two peptides containing tyr656 and tyr711, confirming bromination. Interestingly, mutation of only tyr656, but not ser1395, thr1326 or ser1545, decreased topo IIβ activity, suggesting a functional role for tyr656. These results, while identifying an important tyrosine in topo IIβ, underscore the importance of careful interpretation of modifications having the same nominal mass.
Layered electrophoretic transfer – A method for pre‐analytic processing of histological sections
Authors: Zhu Liang , Tangrea Michael A. , Mukherjee Sumana , Emmert‐Buck Michael R.
Published: January 2011

Current technologies for measuring protein expression across a tissue section are based on MS or in situ detection such as immunohistochemistry. However, due to the inherent molecular complexity of tissue samples and the large dynamic range of protein expression in cells, current approaches are often unable to measure moderate‐ and low‐abundant proteins. In addition, they do not provide information on the physico‐chemical properties of the proteins studied. To address these problems, we are developing a new pre‐analytic methodology termed layered electrophoretic transfer (LET) that selectively separates and processes proteins from an intact tissue section without compromising important two‐dimensional histological information. LET offers two potential advantages over standard techniques: (i) A reduced complexity of the tissue proteome for subsequent analysis; (ii) An opportunity to assess the biochemical status of proteins as they exist in situ. As an initial proof‐of‐concept, we demonstrate here that the protein content from a mixture of molecular weight standards, human tissue lysates, and tissue sections can be successfully transferred and separated using LET, and further demonstrate that the method can be coupled with immunoblotting or MS for downstream measurements. LET technology represents a new pre‐analytic tool for interrogating the proteome in tissue sections while preserving valuable spatial information.
Evaluation of absolute peptide quantitation strategies using selected reaction monitoring
Authors: Campbell James , Rezai Taha , Prakash Amol , Krastins Bryan , Dayon Loïc , Ward Malcolm , Robinson Sarah , Lopez Mary
Published: January 2011

The use of internal peptide standards in selected reaction monitoring experiments enables absolute quantitation. Here, we describe three approaches addressing calibration of peptide concentrations in complex matrices and assess their performance in terms of trueness and precision. The simplest approach described is single reference point quantitation where a heavy peptide is spiked into test samples and the endogenous analyte quantified relative to the heavy peptide internal standard. We refer to the second approach as normal curve quantitation. Here, a constant amount of heavy peptide and a varying amount of light peptide are spiked into matrix to construct a calibration curve. This accounts for matrix effects but due to the presence of endogenous analyte, it is usually not possible to determine the lower LOQ. We refer to the third method as reverse curve quantitation. Here, a constant amount of light peptide and a varying amount of heavy peptide are spiked into matrix to construct a calibration curve. Because there is no contribution to the heavy peptide signal from endogenous analyte, it is possible to measure the equivalent of a blank sample and determine LOQ. These approaches are applied to human plasma samples and used to assay peptides of a set of apolipoproteins.
A comparison of MS2‐based label‐free quantitative proteomic techniques with regards to accuracy and precision
Authors: Colaert Niklaas , Vandekerckhove Joël , Gevaert Kris , Martens Lennart
Published: January 2011

The advent of algorithms for fragmentation spectrum‐based label‐free quantitative proteomics has enabled straightforward quantification of shotgun proteomic experiments. Despite the popularity of these approaches, few studies have been performed to assess their performance. We have therefore profiled the precision and the accuracy of three distinct relative label‐free methods on both the protein and the proteome level. We derived our test data from two well‐characterized publicly available quantitative data sets.
Efficient proteolysis using a regenerable metal‐ion chelate immobilized enzyme reactor supported on organic–inorganic hybrid silica monolith
Authors: Ma Junfeng , Hou Chunyan , Liang Yu , Wang Tingting , Liang Zhen , Zhang Lihua , Zhang Yukui
Published: January 2011

A metal‐ion chelate immobilized enzyme reactor (IMER) supported on organic–inorganic hybrid silica monolith was developed for rapid digestion of proteins. The monolithic support was in situ prepared in a fused silica capillary via the polycondensation between tetraethoxysilane hydrolytic sol and iminodiacetic acid conjugated glycidoxypropyltrimethoxysilane. After activated by Cu2+, trypsin was immobilized onto the monolithic support via metal chelation. Proteolytic capability of such an IMER was evaluated by the digestion of myoglobin and BSA, and the digests were further analyzed by microflow reversed‐phase liquid chromatography with ESI‐MS/MS. Similar sequence coverages of myoglobin and BSA were obtained by IMER, in comparison to those obtained by in‐solution digestion (91 versus 92% for 200 ng myoglobin, and 26 versus 26% for 200 ng BSA). However, the digestion time was shortened from 12 h to 50 s. When the enzymatic activity was decreased after seven runs, the IMER could be easily regenerated by removing Cu2+ via EDTA followed by trypsin immobilization with fresh Cu2+ introduced, yielding the equal sequence coverage (26% for 200 ng BSA). For ∼5 μg rat liver extract, even more proteins were identified with the immobilized trypsin digestion within 150 s in comparison to the in‐solution digestion for 24 h (541 versus 483), demonstrating that the IMER could be a promising tool for efficient and high‐throughput proteome profiling.
Less label, more free: Approaches in label‐free quantitative mass spectrometry
Authors: Neilson Karlie A. , Ali Naveid A. , Muralidharan Sridevi , Mirzaei Mehdi , Mariani Michael , Assadourian Gariné , Lee Albert , van Sluyter Steven C. , Haynes Paul A.
Published: January 2011

In this review we examine techniques, software, and statistical analyses used in label‐free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label‐free quantitation. Limitations of label‐free approaches are considered, label‐free approaches are compared with labelling techniques, and forward‐looking applications for label‐free quantitative data are presented. We conclude that label‐free quantitative proteomics is a reliable, versatile, and cost‐effective alternative to labelled quantitation.
Simulating and validating proteomics data and search results
Authors: Geromanos Scott J. , Hughes Chris , Golick Dan , Ciavarini Steven , Gorenstein Marc V. , Richardson Keith , Hoyes John B. , Vissers Johannes P.C. , Langridge James I.
Published: January 2011

The computational simulation of complete proteomic data sets and their utility to validate detection and interpretation algorithms, to aid in the design of experiments and to assess protein and peptide false discovery rates is presented. The simulation software has been developed for emulating data originating from data‐dependent and data‐independent LC‐MS workflows. Data from all types of commonly used hybrid mass spectrometers can be simulated. The algorithms are based on empirically derived physicochemical liquid and gas phase models for proteins and peptides. Sample composition in terms of complexity and dynamic range, as well as chromatographic, experimental and MS conditions, can be controlled and adjusted independently. The effect of on‐column amounts, gradient length, mass resolution and ion mobility on search specificity will be demonstrated using tryptic peptides from human and yeast cellular lysates simulated over five orders of magnitude in dynamic range. Initial justification of the simulated data sets is achieved by comparing and contrasting the in silico simulated data to experimentally derived results from a 48 protein mixture, spanning a similar magnitude of five orders of magnitude. Additionally, experimental data from replicate and dilutions series experiments will be utilized to determine error rates at the peptide and protein level with respect to mass, area, retention and drift time. The data presented reveal a high degree of similarity at the ion detection, peptide and protein level when analyzed under similar conditions.
The endosomal proteome of macrophage and dendritic cells
Authors: Duclos Sophie , Clavarino Giovanna , Rousserie Gilles , Goyette Guillaume , Boulais Jonathan , Camossetto Voahirana , Gatti Evelina , LaBoissière Sylvie , Pierre Philippe , Desjardins Michel
Published: January 2011

The essential roles of the endovacuolar system in health and disease call for the development of new tools allowing a better understanding of the complex molecular machinery involved in endocytic processes. We took advantage of the floating properties of small latex beads (sLB) on a discontinuous sucrose gradient to isolate highly purified endosomes following internalization of small latex beads in J774 macrophages and bone marrow‐derived dendritic cells (DC). We particularly focused on the isolation of macrophages early endosomes and late endosomes/lysosomes (LE/LYS) as well as the isolation of LE/LYS from immature and lipopolysaccharide‐activated (mature) DC. We subsequently performed a comparative analysis of their respective protein contents by MS. As expected, proteins already known to localize to the early endosomes were enriched in the earliest fraction of J774 endosomes, while proteins known to accumulate later in the process, such as hydrolases, were significantly enriched in the LE/LYS preparations. We next compared the LE/LYS protein contents of immature DC and mature DC, which are known to undergo massive reorganization leading to potent immune activation. The differences between the protein contents of endocytic organelles from macrophages and DC were underlined by focusing on previously poorly characterized biochemical pathways, which could have an unexpected but important role in the endosomal functions of these highly relevant immune cell types.
Quality control in LC‐MS/MS
Authors: Köcher Thomas , Pichler Peter , Swart Remco , Mechtler Karl
Published: January 2011

In the last 15 years, MS‐based protein characterization has expanded at a rapid rate. This success is built upon constantly improving instrumentation and a variety of ingenious methods applied to numerous biological questions. However, the reproducibility of mass spectrometric results is considered by many as insufficient. In part, inadequate quality control might be responsible for the lack of reproducibility. Quality control is rarely discussed in scientific publications. Here, we briefly present measures undertaken in our laboratory to foster a general discussion of the subject.
Statistical issues in quality control of proteomic analyses: Good experimental design and planning
Authors: Cairns David A.
Published: January 2011

Quality control is becoming increasingly important in proteomic investigations as experiments become more multivariate and quantitative. Quality control applies to all stages of an investigation and statistics can play a key role. In this review, the role of statistical ideas in the design and planning of an investigation is described. This involves the design of unbiased experiments using key concepts from statistical experimental design, the understanding of the biological and analytical variation in a system using variance components analysis and the determination of a required sample size to perform a statistically powerful investigation. These concepts are described through simple examples and an example data set from a 2‐D DIGE pilot experiment. Each of these concepts can prove useful in producing better and more reproducible data.
Quality control of nano‐LC‐MS systems using stable isotope‐coded peptides
Authors: Burkhart Julia Maria , Premsler Thomas , Sickmann Albert
Published: January 2011

In analytical sciences, there is a general need for quality control to assess whether a product or a process meets defined requirements. Especially in proteomics, which implies analysis of ten thousands of analytes within a complex mixture, quality control to validate LC‐MS performance and method setup is inevitable to achieve day‐to‐day‐, inter‐system‐, as well as inter‐user reproducibility. Thus, results deriving from LC‐MS analyses can be benchmarked and the need for system maintenance can be revealed. In particular with the advent of label‐free quantification of peptides and proteins, which above all depends on highly stable and reproducible LC separations, HPLC performance has to be appropriately monitored throughout the entire analytical procedure to assure quality and validity of the obtained data. Oftentimes, proteolytic digests of standard proteins are used in this context; however, this approach implies some limitations, such as inadequate batch‐to‐batch reproducibility, limited (if any) dynamic range and compositional inflexibility. Here, we present an alternative strategy of nano‐LC‐MS/MS quality control based on a mixture of synthetic peptides covering the entire LC‐gradient as well as a dynamic range of more than two orders of magnitude. Thus, (i) reproducibility of LC separation, (ii) MS performance (including limit of detection, identification and quantification), as well as (iii) overall nano‐LC‐MS system performance and reproducibility can be routinely monitored even in highly complex samples.
COMPASS: A suite of pre‐ and post‐search proteomics software tools for OMSSA
Authors: Wenger Craig D. , Phanstiel Douglas H. , Lee M. Violet , Bailey Derek J. , Coon Joshua J.
Published: January 2011

Here we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open‐source software pipeline for high‐throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma‐separated value files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC‐MS/MS data sets. The first is a data set of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a data set of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two data sets, COMPASS performs equivalently or better than the current de facto standard, the Trans‐Proteomic Pipeline.
Challenges for proteomics core facilities
Authors: Lilley Kathryn S. , Deery Michael J. , Gatto Laurent
Published: January 2011

Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities.
iTRAQ protein quantification: A quality‐controlled workflow
Authors: Burkhart Julia M. , Vaudel Marc , Zahedi René P. , Martens Lennart , Sickmann Albert
Published: January 2011

Reporter ion‐based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out‐of‐the‐box methods, without thorough quality control. Thus, due to undiscovered limitations of the technique, irrelevant results might be trusted. To address this issue, we here propose a step‐by‐step quality control of the iTRAQ workflow. From sample preparation to final ratio calculation we provide metrics and techniques assessing the actual effectiveness of iTRAQ quantification as well as a novel method for more reliable protein ratio estimation.
Current approaches to the treatment of URTIs in children
Authors: Clarke Ed , Finn Adam
Published: January 2011

Our series Prescribing in children gives practical advice on the management of childhood problems in general practice. Here, the authors discuss the management of upper respiratory tract infections. Copyright © 2010 Wiley Interface Ltd
Bismuth‐metal nanocrystals self‐embedded in high‐k Bi‐based pyrochlore dielectrics grown at room temperature
Authors: Seong Nak‐Jin , Jung Hyun‐June , Yoon Soon‐Gil
Published: January 2011

Bismuth‐metal nanocrystals (NCs) are self‐embedded within high‐k Bi2Mg2/3Nb4/3O7 (BMNO) dielectrics grown at room temperature by rf magnetron sputtering were demonstrated for the low‐voltage nonvolatile memory device. The BMNO pyrochlore films grown in Ar/O2 ambient at room temperature showed the stable dielectric properties, together with high dielectric constant (∼45), small dielectric loss (0.2%), and improved leakage current. Bismuth nanocrystals (a mean size of 2–3 nm) and a high‐k BMNO films (∼50 nm thickness) as a control oxide layer were continuously in situ formed at room temperature in Ar and Ar/O2 ambient, respectively. A significant threshold voltage shift of 0.95 V is observed at a gate voltage of 5 V and the threshold voltage shift linearly increases with increasing gate voltage from 3 to 6 V. The self‐embedded bismuth nanocrystals in high‐k BMNO dielectrics at room temperature represent a viable candidate for low‐voltage NFGM device applications.
Piezoelectric properties and thermal stability of (Na0.53K0.47−xAgx)Nb1−xSbxO3 ceramics
Authors: Zheng Limei , Wang Jinfeng , Wu Qingzao , Zhang Rui , Wang Chunming , Gai Zhigang
Published: January 2011

Many (K1−xNax)NbO3 (KNN)‐based ceramics with high piezoelectric performance exhibit undesirable strong temperature dependence due to the orthorhombic–tetragonal polymorphic phase transition near room temperature. In order to improve the temperature stability of the ceramics, many additives have been added into the KNN‐based ceramics to shift TO–T down to below room temperature. Contrary to the previous approach (Na0.53K0.47−xAgx)Nb1−xSbxO3 (NKANS) ceramics with TO–T well above room temperature have been prepared by a conventional solid‐state reaction method. The density and the electrical properties are effectively improved by the addition of AgSbO3, and optimum piezoelectric properties are found in the ceramics with 0.05 ≤ x ≤ 0.07, with maximum kp ∼ 0.46 for NKANS5 and maximum d33 ∼ 199 pC/N for NKANS7. More importantly, kp remains virtually almost unchanged up to the TO–T temperature (≥100 °C), indicating that the NKANS ceramics exhibit a much improved piezoelectric thermal stability. The analyses suggest that both the high TO–T value and diffuse orthorhombic–tetragonal phase transition should be responsible for the good temperature stability.
Carrier transport of diamond p+‐i‐n+ junction diode fabricated using low‐resistance hopping p+ and n+ layers
Authors: Oyama Kazuhiro , Ri Sung‐Gi , Kato Hiromitsu , Takeuchi Daisuke , Makino Toshiharu , Ogura Masahiko , Tokuda Norio , Okushi Hideyo , Yamasaki Satoshi
Published: January 2011

We have investigated the carrier transport of a single‐crystal diamond p+‐i‐n+ junction diode fabricated using low‐resistance hopping p+ and n+ layers, which showed high‐performance diode characteristics. By comparing the diode characteristics of the p+‐i‐n+ junction with those of the p+‐n+ diode and metal/n+/metal structure, the following results were obtained. The carrier transport of the p+‐i‐n+ junction is described using the band conduction caused by the free carriers, although the current transport in both p+ and n+ layers is mainly by the hopping conduction. The i‐layer in the p+‐i‐n+ junction provides a low‐resistance layer for the forward current and a good blocking layer for the reverse current. The contact resistance of the n+/metal layer affects the carrier transport of the p+‐i‐n+ diode, which lacks the ohmic property even with the phosphorous concentration around 1020 cm−3.
Finite size effects in ZnO nanoparticles: An electron paramagnetic resonance (EPR) analysis
Authors: Jakes Peter , Erdem Emre
Published: January 2011

ZnO nanoparticles were synthesized by solid coprecipitation method with consecutive high energy ball milling procedure. By reducing the particle size of ZnO to nano dimensions strong nano‐size effects were observed. In order to characterize the ZnO defect structure, EPR has been applied. It was observed that below 50 nm the surface defects play a dominant role in the electronic properties of ZnO. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Direct‐current nanogenerator based on ZnO nanotube arrays
Authors: Xi Y. , Lien D. H. , Yang R. S. , Xu C. , Hu C. G.
Published: January 2011

Due to the special structure of a nanotube (NT), the different potential from piezoelectricity can be naturally divided by the hollow of the tube when the NT is bent or deformed. Furthermore, both the bent/deformed inner and outer wall can form a steady voltage/current, which might enhance the output voltage/current. We demonstrate a direct‐current nanogenerator (NG) based on zinc oxide (ZnO) NT arrays driven by an ultrasonic wave. The average output voltage is ca. 0.10 mV and the current density is ca. 0.069 μA/mm2. Our study shows that the maximum power output of the ZnO NT array NG is 0.112 nW and the power density is 1.4 nW/cm2. The success of energy harvesting from ZnO NTs reveals the potential of using nanogenerators for tubular piezoelectric materials. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)