bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic approaches to the analysis of multiprotein signaling complexes
Authors: Yang Wei , Steen Hanno , Freeman Michael R. 
Published: February 2008

AbstractSignal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.
Proteomics, nanotechnology and molecular diagnostics
Authors: Johnson Christopher J. , Zhukovsky Nikolay , Cass Anthony E. G. , Nagy Judit M. 
Published: February 2008

AbstractSequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.
Protein networking: insights into global functional organization of proteomes
Authors: Pieroni Enrico , de la Fuente van Bentem Sergio , Mancosu Gianmaria , Capobianco Enrico , Hirt Heribert , de la Fuente Alberto 
Published: February 2008

AbstractThe formulation of network models from global protein studies is essential to understand the functioning of organisms. Network models of the proteome enable the application of Complex Network Analysis, a quantitative framework to investigate large complex networks using techniques from graph theory, statistical physics, dynamical systems and other fields. This approach has provided many insights into the functional organization of the proteome so far and will likely continue to do so. Currently, several network concepts have emerged in the field of proteomics. It is important to highlight the differences between these concepts, since different representations allow different insights into functional organization. One such concept is the protein interaction network, which contains proteins as nodes and undirected edges representing the occurrence of binding in large‐scale protein‐protein interaction studies. A second concept is the protein‐signaling network, in which the nodes correspond to levels of post‐translationally modified forms of proteins and directed edges to causal effects through post‐translational modification, such as phosphorylation. Several other network concepts were introduced for proteomics. Although all formulated as networks, the concepts represent widely different physical systems. Therefore caution should be taken when applying relevant topological analysis. We review recent literature formulating and analyzing such networks.
Adaptive expression of foreign genes in the clonal variants of bacteria: From proteomics to clinical application
Authors: Sriramulu Dinesh D. 
Published: February 2008

AbstractClonal variants of bacteria are able to colonize environmental niches and patients. The factors, that determine the interplay between the colonization of diverse habitats and adaptation, are acquired through horizontal gene transfer. Elucidation of mechanisms, which lead to the prevalence of dominant bacterial clones in patients and the environment, requires the knowledge of complex phenotypes. It was found in the genomes of most bacteria, that upon a conserved chromosomal backbone there were regions of plasticity achieved by insertions, deletions and rearrangements of genomic islands and islets as well as large chromosomal inversions. However, it had been shown that environmental and clinical isolates are indistinguishable in certain pathogenic and biodegradative properties. For example, clonal variants of Pseudomonas aeruginosa exhibit convergent phenotypes despite the presence of numerous DNA insertions in the genome. Apart from this feature, expression of a few genes from the acquired genetic material is important for niche‐based adaptation of this organism. Protein expression patterns at the cellular and sub‐cellular levels showed common virulence factors and novel drug targets among clonal variants of bacteria. This review will give a short overview on proteomics of different clonal variants of bacteria with respect to clinical applications.
Synthesis and crosslinking behavior of a novel linear polymer bearing 1,2,3‐triazol and benzoxazine groups in the main chain by a step‐growth click‐coupling reaction
Authors: Nagai Atsushi , Kamei Yasutaka , Wang Xiao‐Shui , Omura Masaki , Sudo Atsushi , Nishida Haruo , Kawamoto Eiichi , Endo Takeshi 
Published: February 2008

AbstractThe click‐coupling reaction was applied to polycondensation, to synthesize a high‐molecular weight prepolymer having benzoxazine moieties in the main chain. For the polycondensation, a bifunctional N‐propargyl benzoxazine was synthesized from bisphenol A, propargylamine, and formaldehyde. The propargyl group was efficiently used for the copper(I)‐catalyzed alkyne‐azide “click” reaction with p‐xylene‐α,α′‐diazide, to give the corresponding linear polycondensate having 1,2,3‐triazole junctions. The polycondensation proceeded in N,N‐dimethylformamide (DMF) at room temperature. By this highly efficient “click‐” polycondensation reaction, the benzoxazine ring in the monomer was successfully introduced into the polymer main chain without any side reaction. The obtained polymer (=prepolymer) underwent thermal crosslinking to afford the corresponding product, which was insoluble in a wide range of organic solvents and exhibited higher thermal stability than the polymer before crosslinking. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2316–2325, 2008
Facile fabrication of hybrid nanoparticles surface grafted with multi‐responsive polymer brushes via block copolymer micellization and self‐catalyzed core gelation
Authors: Zhang Yanfeng , Gu Weiyin , Xu Hangxun , Liu Shiyong 
Published: February 2008

AbstractPoly(2‐(dimethylamino)ethyl methacrylate)‐b‐poly(γ‐methacryloxypropyl‐trimethoxysilane) (PDMA‐b‐PMPS) was synthesized via consecutive reversible addition‐fragmentation chain transfer (RAFT) polymerizations in 1,4‐dioxane. Subsequent micellization of the obtained amphiphilic diblock polymer in aqueous solution led to the formation of nanoparticles consisting of hydrophobic PMPS cores and well‐solvated PDMA shells. Containing tertiary amine residues, PDMA blocks in micelle coronas can spontaneously catalyze the sol–gel reactions of trimethoxysilyl groups within PMPS cores, leading to the formation of hybrid nanoparticles coated with PDMA brushes. Transmission electron microscopy (TEM) and laser light scattering (LLS) revealed the presence of monodisperse spherical hybrid nanoparticles, and the grafting density of PDMA chains at the surface of nanoparticle cores was estimated to be ∼5.8 nm2/chain. PDMA brushes exhibit dual stimuli‐responsiveness, and the swelling/collapse of them can be finely tuned with solution pH and temperatures. The obtained multi‐responsive hybrid nanoparticles might find potential applications in fields such as smart devices, recyclable catalysts, and intelligent nanocarriers for drug delivery or gene transfection. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2379–2389, 2008
Tadpole‐shaped amphiphilic copolymers prepared via RAFT polymerization and click reaction
Authors: Shi Gang‐Yin , Tang Xue‐Zhi , Pan Cai‐Yuan 
Published: February 2008

AbstractThe tadpole‐shaped amphiphilic copolymers with cyclic polystyrene as the head and a linear poly(N‐isopropylacrylamide) as the tail have been successfully synthesized by combination of reversible addition‐fragmentation chain transfer (RAFT) polymerization and “click” reaction. The synthesis involves two main steps: (1) preparation of a linear acetylene‐terminated PNIPAAM‐b‐PS with a side azido group anchored at the junction between two blocks; (2) intramolecular cyclization reaction to produce the cyclic PS block using “click” chemistry under high dilution. The structures, molecular weights, and molecular weight distributions of the resulted intermediates and the target polymers were characterized by their 1H NMR, FTIR, and gel permeation chromatography. The difference of surface property between tadpole‐shaped polymer and its linear precursor was observed, and the water contact angles on the former surface are larger than that of the latter surface. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2390–2401, 2008
Energetic polymer salts from 1‐vinyl‐1,2,4‐triazole derivatives
Authors: Xue Hong , Gao Haixiang , Shreeve Jean'ne M. 
Published: February 2008

AbstractEnergetic polymers salts from 1‐vinyl‐1,2,4‐triazole derivatives have been synthesized via free radical polymerization of 1‐vinyl‐1,2,4‐triazolium monomer salts or by protonation of poly(1‐vinyl‐1,2,4‐triazole) with inorganic or organic acids. Standard enthalpies of formation of the new monomer salts were calculated using the computationally feasible DFT(B3LYP) and MP2 methods in conjunction with an empirical approach based on densities of salts. Compared with the monomer salts, the polymer salts have good thermal properties with high densities > 1.5 g cm−3. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2414–2421, 2008
Synthesis and characterization of fluorescently labeled core cross‐linked star polymers
Authors: Spiniello Marisa , Blencowe Anton , Qiao Greg G. 
Published: February 2008

AbstractA series of fluorescently labeled core cross‐linked star (CCS) polymers were synthesized via the “arm‐first” approach, employing atom transfer radical polymerization (ATRP) to control the resulting architecture. The initiator p‐toluenesulfonyl chloride (TsCl) was used to synthesize “living” poly(methyl methacrylate) (PMMA) macroinitiator, which was subsequently cross‐linked to generate the CCS polymers. Divinylbenzene (DVB) was used as the cross‐linker and 7‐[4‐(trifluoromethyl)coumarin] methacrylamide (F1, λex = 343 nm) was added as a fluorescent labeling monomer. A range of PMMA/DVB/F1 based CCS polymers were synthesized with the core domain made selectively fluorescent by using varying amounts of monomer F1. The core functionalized stars were characterized using gel permeation chromatography (GPC) equipped with multi‐angle laser light scattering (MALLS), refractive index (RI), and UV–visible detectors. The fluorescence quantum yield (ΦF) and the amount of fluorescent monomer incorporated into the core were quantified by UV–visible and fluorescence spectrophotometry. It was recognized that the overall molecular weights of the stars produced, along with their core molecular weight, decreased as the mol % of monomer F1 was increased relative to cross‐linker. Visual confirmation of F1 incorporation was obtained by fluorescence microscopy of thin polymer films cast on glass substrates. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2422–2432, 2008
Creating microenvironments using encapsulated polymers
Authors: Kobašlija Muris , Bogdan Andrew R. , Poe Sarah L. , Escobedo Fernando , Mcquade D. Tyler 
Published: February 2008

AbstractMiscible solvents are phase separated within microcapsules containing entrapped polymers, thereby creating stable, isolated microenvironments. In particular, we demonstrate that encapsulated polyethyleneimine induces phase separation of toluene and methanol and that this phase separation is well modeled by the Flory‐Huggins theory. We further show the generality of microenvironment formation by phase separating tetrahydrofuran and acetone with entrapped polystyrene. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2309–2315, 2008
Morphological changes of BTDA/m‐PDA polyimide banded spherulites: The effect of solvent on banding
Authors: Zhang Ruibin , Liu Xiangyang , Gu Yi 
Published: February 2008

AbstractBTDA/m‐PDA polyimide banded spherulites with different band spacing were observed in the same sandwiched film. Atom force microscopy (AFM) analysis suggested that the banded structure was caused by periodic twisting of radial grown lamella bundles. Based on polarizing light microscopy (PLM) and AFM observation, it was found that spherulites grown near the center of the film exhibited bigger band spacing and consisted of wider lamellae compared with those grown near the fringe, which was suggested to be caused by different solvent amount during imidization and crystallization: the more solvent existed, the wider the lamella would grow and the bigger the band spacing would be. It was further proved by changing the film thickness and PAA solution concentration. SEM observation showed that when crystallized in the solution, the lamella became ultra thick and straight, and formed small particles. Powder X‐ray diffraction revealed that crystal structures of the banded spherulite and the small particle were identical or at least very similar. Another solvent with lower boiling point was used in sample preparation, however, under the same preparation conditions, the grown features of banded spherulites did not change. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 659–667, 2008
Dielectric layers for organic field effect transistors as gate dielectric and surface passivation
Authors: Diekmann T. , Pannemann C. , Hilleringmann U. 
Published: February 2008

AbstractOrganic field effect transistors with the organic semiconductor pentacene, using silicon substrates, were successfully built on conventional inorganic dielectrics like silicon dioxide or silicon nitride. They can drive drain currents up to 15 mA. Beyond that, polymer films were investigated as gate dielectrics in order to achieve transistors on plastic films. On polyester substrates with an inorganic–organic gate dielectric, devices reach drain currents comparable to transistors on silicon dioxide and charge carrier mobilities of up to 0.35 cm2/V s. Analysis of the pentacene surface by atomic force microscopy showed pentacene crystallites achieving dimensions of more than 1.5 µm. The unprotected organic devices suffer from degradation due to water and oxygen incorporation. Therefore, the application of a hydrophobic polytetrafluoroethylene layer as capping layer is studied. Because of the reduced influence of water, a shift to positive threshold voltages is caused. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Assembly, structure, and performance of an ultra‐thin film organic field‐effect transistor (OFET) based on substituted oligothiophenes
Authors: Haubner K. , Jaehne E. , Adler H.‐J. P. , Koehler D. , Loppacher C. , Eng L. M. , Grenzer J. , Herasimovich A. , Scheinert S. 
Published: February 2008

AbstractWe report on the improved assembly and characterization of a small molecule organic field‐effect transistor (OFET). Novel α,ω‐dicyano substituted β,β′‐dibutylquaterthiophene molecules (DCNDBQT) were synthesized and characterized by UV–Vis spectroscopy, differential scanning calorimetry, thermal gravimetric analysis and cyclic voltammetry. The ultra‐thin organic film formation on TiO2 templates was effectively promoted through the specifically designed bifunctional self assembly molecules (SAM) 5‐cyano‐2‐(butyl‐4‐phosphonic acid)‐3‐butylthiophene (CNBTPA). Excellent structural properties were found for up to 9 DCNDBQT molecule thick films prepared through UHV vacuum sublimation as investigated with UHV non‐contact atomic force microscopy (nc‐AFM) and X‐ray diffraction. Both X‐ray and nc‐AFM data indicate that the DCNDBQT molecules form a well‐ordered terraced structure exhibiting step heights of 1.5 nm to 2.0 nm layers. Hence, the DCNDBQTmolecules are linked to the functional SAM interface layer by H‐bond interactions (see structure model) standing quasi perpendicular to the TiO2 template, and thus providing optimal orbital overlap neigh‐bouring thiophene rings.The vacuum sublimated DCNDBQT molecules form a closed packed and dense molecular layer that was used to construct and operate a nanoscopic OFET‐structure. The resulting field mobilities of 10–5 cm2 V–1 s–1 reflect a high current density in our ultrathin but highly ordered structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microscopic and spectroscopic characterization of interfaces and dielectric layers for OFET devices
Authors: Müller K. , Burkov Y. , Mandal D. , Henkel K. , Paloumpa I. , Goryachko A. , Schmeißer D. 
Published: February 2008

AbstractThe functionality of organic devices is strongly influenced by their interfaces. We report on new microscopic methods for interface characterization of organic devices in operation mode. With photoemission electron microscopy (PEEM), a direct mapping of charge carrier density is possible. Microscopy in the scanning Kelvin force mode (SKPM) gives information about the local surface potential. In addition to lateral information, depth profiling of interface chemistry is important. As an example, we present a study of the electrode/dielectric layer interface, performed using photoelectron spectroscopy. This interface is of technological relevance for organic memories, based on organic field effect transistors (OFETs). The dielectric part is made of ferroelectric polymers like poly(vinylidene fluoride‐trifluoroethylene) (P(VDF‐TrFE)). We compare aluminium/P(VDF‐TrFE) and PEDOT:PSS/P(VDF‐TrFE) interfaces (PEDOT:PSS is the conductive polymer poly(3,4‐ethylenedioxythiophene):polystyrenesulphonate). Finally we present memory elements consisting of metal ferroelectric insulator semiconductor (MFIS) and OFET structures. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Scaling limits and MHz operation in thiophene‐based field‐effect transistors
Authors: Hoppe A. , Balster T. , Muck T. , Wagner V. 
Published: February 2008

AbstractTo achieve high performance organic field effect transistors (OFETs) with enhanced currents, high switching speeds and improved integration density the channel length L is downscaled to the sub‐micrometer regime. The influence of important scaling parameters on the electrical performance of bottom contact devices is analyzed. High‐mobility oligo‐ and polythiophenes were used as semiconductor, which combine the advantages of highly ordered growth with processibility from solution. Devices with optimized parameters exhibit high switching frequencies beyond 2 MHz. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fundamental interface properties in OFETs: Bonding, structure and function of molecular adsorbate layers on solid surfaces
Authors: Soubatch S. , Temirov R. , Tautz F. S. 
Published: February 2008

AbstractThe functionality of organic field effect transistors resides in their interfaces. Highly ordered molecular adsorbate layers provide an excellent tool to study the relevant physical properties of these interfaces. In this article we focus on molecules at the organic/metal interface. We find that their geometry and electronic structure are very responsive to influences from the substrate and the molecular environment, while interface structures evolve cooperatively in the sway of interfacial and intermolecular interactions and can thus be extremely complex. Although our results cannot be transferred directly to real devices, a number of intriguing physical effects emerge that could play an important role in (nanoscale) OFETs, e.g. an anomalously strong energy band dispersion at the organic/metal interface, a remarkable plasticity of the electronic structure of molecules in ultra‐thin films, and Kondo physics in a non‐magnetic molecular wire. Finally, we report the realization of a mechanically gated single‐molecule transistor that allows investigating the transport physics in a molecular wire as a function of contact properties. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Liquid chromatography/triple quadrupole tandem mass spectrometry with multiple reaction monitoring for optimal selection of transitions to evaluate nutraceuticals from olive‐tree materials
Authors: Luján Rafael Japón , Capote Feliciano Priego , Marinas Alberto , de Castro María Dolores Luque 
Published: February 2008

AbstractOptimal transitions have been selected for the identification and quantitation of the most interesting hydrophilic biophenols in extracts from olive‐tree materials, which are of interest because of their nutraceutical properties. The tested materials were extra virgin olive oil, waste from oil production (known as alperujo), and olive‐tree materials such as leaves, small branches and fruit stones. The identification and determination steps of the target biophenols are based on liquid chromatography/tandem mass spectrometry (LC/MS/MS) with a triple quadrupole (QQQ) mass detector. The interface between the chromatograph and the QQQ was an electrospray ionization source operated in the negative ion mode. Highly selective identification of the biophenols was confirmed by multiple reaction monitoring (MRM) using the most representative transitions from the precursor ion to the different product ions. Quantitative MS/MS analysis was carried out by optimization and selection of the most sensitive transition for each analyte, which resulted in estimated detection limits of 5.10 to 11.65 ng/mL for the extracts. The biophenols were extracted from the tested samples by different methods: liquid‐liquid extraction for virgin olive oil, microwave‐assisted leaching for olive leaves, branches and stones, and pressurized liquid leaching for alperujo. This study provides valuable information about the most suitable source for the isolation of each nutraceutical biophenol and enables us to obtain a complete profile of them in Olea Europaea. Copyright © 2008 John Wiley & Sons, Ltd.