bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProteomeGRID: towards a high‐throughput proteomics pipeline through opportunistic cluster image computing for two‐dimensional gel electrophoresis
Authors: Dowsey Andrew W. , Dunn Michael J. , Yang Guang‐Zhong 
Published: October 2004

AbstractThe quest for high‐throughput proteomics has revealed a number of critical issues. Whilst improved two‐dimensional gel electrophoresis (2‐DE) sample preparation, staining and imaging issues are being actively pursued by industry, reliable high‐throughput spot matching and quantification remains a significant bottleneck in the bioinformatics pipeline, thus restricting the flow of data to mass spectrometry through robotic spot excision and protein digestion. To this end, it is important to establish a full multi‐site Grid infrastructure for the processing, archival, standardisation and retrieval of proteomic data and metadata. Particular emphasis needs to be placed on large‐scale image mining and statistical cross‐validation for reliable, fully automated differential expression analysis, and the development of a statistical 2‐DE object model and ontology that underpins the emerging HUPO PSI GPS (Human Proteome Organization Proteomics Standards Initiative General Proteomics Standards. The first step towards this goal is to overcome the computational and communications burden entailed by the image analysis of 2‐DE gels with Grid enabled cluster computing. This paper presents the proTurbo framework as part of the ProteomeGRID, which utilises Condor cluster management combined with CORBA communications and JPEG‐LS lossless image compression for task farming. A novel probabilistic eager scheduler has been developed to minimise make‐span, where tasks are duplicated in response to the likelihood of the Condor machines' owners evicting them. A 60 gel experiment was pair‐wise image registered (3540 tasks) on a 40 machine Linux cluster. Real‐world performance and network overhead was gauged, and Poisson distributed worker evictions were simulated. Our results show a 4:1 lossless and 9:1 near lossless image compression ratio and so network overhead did not affect other users. With 40 workers a 32× speed‐up was seen (80% resource efficiency), and the eager scheduler reduced the impact of evictions by 58%.
Proteomic analysis of melanoma‐derived exosomes by two‐dimensional polyacrylamide gel electrophoresis and mass spectrometry
Authors: Mears Rainy , Craven Rachel A. , Hanrahan Sarah , Totty Nick , Upton Carol , Young Sarah L. , Patel Poulam , Selby Peter J. , Banks Rosamonde E. 
Published: October 2004

AbstractExosomes are 40–100 nm vesicles released by numerous cell types and are thought to have a variety of roles depending on their origin. Exosomes derived from antigen presenting cells have been shown to be capable of initiating immune responses in vivo and eradicating established tumours in murine models. Tumour‐derived exosomes can be utilised as a source of tumour antigen for cross‐priming to T‐cells and are thus of interest for use in anti‐tumour immunotherapy. Further exploration into the protein composition of exosomes may increase our understanding of their potential roles in vivo and this study has examined the proteome of exosomes purified from cell supernatants of the melanoma cell lines MeWo and SK‐MEL‐28. The vesicular nature and size (30–100 nm) of the purified exosomes was confirmed by electron microscopy and sucrose density gradient centrifugation. Western blotting demonstrated the absence of calnexin and cytochrome c, verifying the purity of the exosome preparations, as well as enrichment of MHC class I and the tumour‐associated antigens Mart‐1 and Mel‐CAM. The two‐dimensional polyarcylamide gel electrophoresis (2‐D PAGE) protein profiles of exosomes from the two cell lines were highly comparable and strikingly different from the profiles of the total cell lysates. Mass spectrometric sequencing identified proteins present in 49 protein spots in the exosome lysates. Several of these have been identified previously in exosomes but some are novel, including p120 catenin, radixin, and immunoglobulin superfamily member 8 (PGRL). Proteins present in whole‐cell lysates that were significantly reduced or excluded from exosomes were also identified and included several mitochondrial and lysosomal proteins, again confirming the proposed endosomal origin of exosomes. This study presents a starting point for future more in‐depth protein studies of tumour‐derived exosomes which will aid the understanding of their biogenesis and targeting for use in anti‐tumour immunotherapy protocols.
Proteomic analysis of the response of Arabidopsis chloroplast proteins to high light stress
Authors: Phee Bong‐Kwan , Cho Jin‐Hwan , Park Sebyul , Jung Jin Hee , Lee Youn‐Hyung , Jeon Jong‐Seong , Bhoo Seong Hee , Hahn Tae‐Ryong 
Published: October 2004

AbstractLight is an essential environmental factor in the progression of plant growth and development but prolonged exposure to high levels of light stress can cause cellular damage and ultimately result in the death of the plant. Plants can respond defensively to this stress for a limited period and this involves changes to their gene expression profiles. Proteomic approaches were therefore applied to the study of the response to high light stress in the Arabidopsis thaliana plant species. Wild‐type Arabidopsis was grown under normal light (100 μmol photons·m−2·s−1) conditions and then subjected to high light (1000 μmol photons·m−2·s−1) stress. Chloroplasts were then isolated from these plants and both soluble and insoluble proteins were extracted and subjected to two‐dimensional (2‐D) gel electrophoresis. The resolved proteins were subsequently identified by matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) and comparative database analysis. 64 protein spots, which were identified as candidate factors that responded to high light stress, were then selected for analysis and 52 of these were successfully identified using MALDI‐TOF‐MS analysis. 35 of the 52 identified proteins were found to decrease their expression levels during high light stress and a further 14 of the candidate proteins had upregulated expression levels under these conditions. Most of the proteins that were downregulated during high light stress are involved in photosynthesis pathways. However, many of the 14 upregulated proteins were identified as previously well‐known high light stress‐related proteins, such as heat shock proteins (HSPs), dehydroascorbate reductase (DHAR), and superoxide dismutase (SOD). Three novel proteins that were more highly expressed during periods of high light stress but had no clear functional relationship to these conditions, were also identified in this study.
Proteomic analysis of pathogen‐responsive proteins from rice leaves induced by rice blast fungus,Magnaporthe grisea
Authors: Kim Sun Tae , Kim Sang Gon , Hwang Du Hyeon , Kang Sun Young , Kim Han Ju , Lee Byung Hyun , Lee Jeung Joo , Kang Kyu Young 
Published: October 2004

AbstractProteomic approaches using two‐dimensional gel electrophoresis (2‐DE) were adopted to identify proteins from rice leaf that are differentially expressed in response to the rice blast fungus,Magnaporthe grisea. Microscopic observation of inoculated leaf withM. grisearevealed that callose deposition and hypersensitive response was clearly visible in incompatible interactions but excessive invading hypha with branches were evident in compatible interactions. Proteins were extracted from leaves 24, 48, and 72 hours after rice blast fungus inoculation. Eight proteins resolved on the 2‐DE gels were induced or increased in the inoculated leaf. Matrix‐assisted laser desorption/ionization‐time of flight analysis of these differentially displayed proteins showed them to be two receptor‐like protein kinases (RLK), two β‐1.3‐glucanases (Glu1, Glu2), thaumatin‐like protein (TLP), peroxidase (POX 22.3), probenazole‐inducible protein (PBZ1), and rice pathogenesis‐related 10 (OsPR‐10). Of these proteins, RLK, TLP, PBZ, and OsPR‐10 proteins were induced more in the incompatible interactions than in compatible ones. A phytohormone, jasmonic acid also induced all eight proteins in leaves. To confirm whether the expression profile is equal to the 2‐DE data, seven cDNA clones were used as probes in Northern hybridization experiments using total RNA from leaf tissues inoculated with incompatible and compatible rice blast fungal races. The genes encodingPOX22.3,Glu1,Glu2,TLP,OsRLK,PBZ1, andOsPR‐10 were activated in inoculated leaves, withTLP,OsRLK,PBZ1, andOsPR‐10 being expressed earlier and more in incompatible than in compatible interactions. These results suggest that early and high induction of these genes may provide host plants with leading edges to defend themselves. The localization of two rice PR‐10 proteins, PBZ1 and OsPR‐10, was further examined by immunohistochemical analysis. PBZ1 accumulated highly in mesophyll cells under the attachment site of the appressorium. In contrast, OsPR‐10 expression was mainly localized to vascular tissue.
Polymerization in magnetic field. XVI. Kinetic aspects regarding methyl methacrylate polymerization in high magnetic field
Authors: Chiriac Aurica P. 
Published: October 2004

AbstractThe effect of a high magnetic field of 7 T in the reaction of methyl methacrylate polymerization is emphasized. The intervening magnetokinetic modifications are correlated with the system of radical initiation with benzoyl peroxide, 2,2′‐azobis(2‐methylpropionitrile), 4,4′‐azobis(4‐cyanopentanoic acid), and 1,1′‐azobis(cyclohexane‐1‐carbonitrile). The characterization of the synthesized polymers is correlated with the reaction conditions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5678–5686, 2004
Preparation and characterization of acrylic‐based black particles of poly(methyl methacrylate‐co‐ethylene glycol dimethacrylate) by dispersion polymerization for electrophoretic displays
Authors: Yu Dong‐Guk , An Jeong Ho 
Published: October 2004

AbstractUltrafine black particles, ranging in diameter from 1 to 3 μm, were prepared by dispersion polymerization in a methanol/water mixture with vinyl monomers, nonpolymerizable Sudan black B dyes, and fluorescein isothiocyanate labeled charge control additives. Both the ratio of the methanol to the water dispersion medium and the polymeric stabilizer concentration had significant effects on the particle size. The important role of the stabilizer concentration lay in the particle formation step, during which it determined the particle stability and final particle size. These could affect the extent of the aggregation of nuclei by changing the adsorption rate of the stabilizer and the viscosity of the dispersion medium, resulting in smaller particles. The fluorescent‐labeled charge control additives strongly affected the electrophoretic mobility. A small concentration of fluorescent‐labeled charge control additives increased the electrophoretic mobility. However, a further addition reduced the electrophoretic mobility of the polymer particles. The concentration dependence of the fluorescent‐labeled charge control additives on the deposition behavior in the polymer particles was successfully imaged and thereafter quantified by image analysis. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5608–5616, 2004
Free‐radical polymerization of methyl methacrylate with a tetrafunctional peroxide initiator
Authors: Scorah M. J. , Dhib R. , Penlidis A. 
Published: October 2004

AbstractThis study examined the use of a new tetrafunctional peroxide initiator in the bulk free‐radical polymerization of methyl methacrylate. The objective was to investigate the effect of using a multifunctional initiator through an examination of the rates of polymerization and the polymer properties. The molecular weights and radii of gyration were obtained with a size exclusion chromatograph equipped with an online multi‐angle laser light scattering detector. The performance of the tetrafunctional initiator was compared to that of a monofunctional counterpart [tert‐butylperoxy 2‐ethylhexyl carbonate (TBEC)]. The results showed that the new tetrafunctional peroxide initiator produced a faster rate of polymerization than TBEC at an equivalent concentration but also generated a polymer of a lower molecular weight. This trend was the opposite of what was observed in a previous study with styrene. When TBEC was used at a concentration four times that of the new tetrafunctional peroxide initiator, both produced equal rates of polymerization and similar molecular weights. The degree of branching was also investigated with radius‐of‐gyration plots. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5647–5661, 2004
Synthesis and characterization of novel poly(cycloalkyl methacrylate) bearing fused‐ring structure and its copolymers
Authors: Asha S. K. , Deepthimol V. , Lekshmi M. 
Published: October 2004

AbstractA new family of cycloaliphatic fused‐ring acrylic polymers based on 8‐hydroxymethyltricyclo[5.2.1.02,6]decane (TCD) has been synthesized by free‐radical polymerization. TCD‐methacrylate (TCD‐MA) was synthesized by reacting TCD with methacrylic acid in toluene via transesterification with p‐toluenesulfonic acid as a catalyst. TCDMA was polymerized in toluene with benzoyl peroxide as a free‐radical initiator at 80 °C. Copolymers were synthesized by polymerizing TCDMA with styrene and methyl methacrylate. The composition of the comonomers was varied from 0 to 100%. Homo‐ and copolymers were characterized by Fourier transform infrared (FTIR) and 13C NMR spectroscopy. Molecular weight determination by gel permeation chromatography showed that the polymers were obtained in very high molecular weights in the range of Mn > 50,000 and Mw > 80,000 with relatively low polydispersity. The composition analysis of both the copolymer series were determined by 1H NMR. The thermal properties of the homo‐ and copolymers were studied with differential scanning calorimetry and all the polymers were found to be amorphous. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5617–5626, 2004
Dithiocarbamate mediated controlled/living free radical polymerization of methyl acrylate under 60Co γ‐ray irradiation: Conjugation effect of N‐group
Authors: Hua Daoben , Bai Ruke , Lu Weiqi , Pan Caiyuan 
Published: October 2004

AbstractThe free radical polymerizations of methyl acrylate have been studied under γ‐ray irradiation in the presence of the dithiocarbamates with different N‐groups. The results indicate that the conjugation structure of the N‐group of dithiocarbamate plays an important role in living free radical polymerization. The polymerizations reveal good living characteristics in the presence of dithiocarbamates (benzyl 1H‐imidazole‐1‐carbodithioate, benzyl 1H‐pyrrole‐1‐carbodithioate, benzyl 1H‐indole‐1‐carbodithioate, and benzyl 9H‐carbazole‐9‐carbodithioate) with N‐aryl group. In contrast, the polymerization with benzyl N,N‐diethyldithiocarbamate cannot be controlled, and the obtained polymer has a broad molecular weight distribution or even crosslink occurs. Moreover, polymerization rate is influenced by the conjugation structure of the N‐group of dithiocarbamate, and the aromatic polycyclic structure of the N‐group leads to slow polymerization. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5670–5677, 2004
Synthesis and adsorption properties of gold nanoparticles within pores of surface‐functional porous polymer microspheres
Authors: Kim Yong‐Jin , Kim Jin‐Woong , Lee Jung‐Eun , Ryu Jee‐Hyun , Kim Junoh , Chang Ih‐Seop , Suh Kyung‐Do 
Published: October 2004

AbstractMesoporous polymer microspheres with gold (Au) nanoparticles inside their pores were prepared considering their surface functionality and porosity. The Au/polymer composite microspheres prepared were characterized by transmission electron microscope (TEM), X‐ray diffraction (XRD), and Brunauer–Emmett–Teller (BET) techniques. The results showed that the adsorption of Au nanoparticles could be increased by imparting the pore structure and surface‐functional groups into the supporting polymer microspheres (in this study, poly (ethylene glycol dimethacrylate‐co‐acrylonitrile) and poly (EGDMA‐co‐AN) system). Above all, from this study, it was established that the porosity of the polymer microspheres is the most important factor that determines the distribution and adsorption amount of face‐centered cubic (fcc) Au nanoparticles in the final products. Our study showed that the continuous adsorption of Au nanoparticles with the aid of the large surface area and surface interaction sites formed more favorably the Au/polymer composite microspheres. The BET measurements of Au/poly(EGDMA‐co‐AN) composite microspheres reveals that the adsorption of Au nanoparticles into the pores kept the pore structure intact and made it more porous. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5627–5635, 2004
Synthesis of polyethylene with bimodal molecular weight distribution by supported iron‐based catalyst
Authors: Li Lidong , Wang Qi 
Published: October 2004

AbstractThrough immobilization of two iron‐based complexes, [((2,6‐MePh)N = C(Me))2C5H3N]FeCl2 (1) and [((2,6‐iPrPh)N = C(Me))2C5H3N]FeCl2 (2), on SiO2 pretreated with tetraethylaluminoxane (TEAO), two supported iron‐based catalysts, 1/TEAO/SiO2 (3) and 2/TEAO/SiO2 (4), were prepared. These two supported catalysts 3 and 4 could be used to catalyze ethylene polymerization with moderate polymerization activity and prepare linear high‐density polyethylene with bimodal molecular weight distribution (MWD). It was demonstrated that immobilization of catalyst could significantly improve molecular weight (MW) of high‐MW fraction of the resultant polyethylene, as well as maintain bimodal MWD of polyethylene produced by the corresponding homogeneous catalysts. Such bimodal MWD of polyethylene produced by supported iron‐based catalysts could be well tailored by varying polymerization conditions, such as ethylene pressure and molar ratio of Al to Fe. It has been proven that TEAO is an efficient activator for both homogeneous and heterogeneous iron‐based catalysts for producing polyethylene with bimodal MWD. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5662–5669, 2004
Transitional flow behavior of entangled polyisoprene solutions
Authors: Philips Amy , Wang Shi‐Qing 
Published: October 2004

AbstractA contradiction has recently appeared between the current understanding of entangled polymers in nonlinear shear flow and new experimental observations based on highly entangled monodisperse 1,4‐polybutadiene solutions. Using entangled polydisperse solutions, we have examined the universality of the new revelation that any sufficiently entangled and relatively monodisperse polymeric fluids undergo a flow transition in simple shear when the applied stress is comparable to the plateau modulus. Indeed, a similar flow transition, marking the onset of bulk chain disentanglement, as previously observed for polybutadiene solutions in controlled‐stress experiments, can also be observed in less entangled and more polydisperse polyisoprene solutions, whereas controlled‐rate experiments do not reveal any transitional behavior. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4132–4138, 2004
Combined effects of clay modifications and compatibilizers on the formation and physical properties of melt‐mixed polypropylene/clay nanocomposites
Authors: Chiu Fang‐Chyou , Lai Sun‐Mou , Chen Jong‐Wu , Chu Pei‐Hsien 
Published: October 2004

AbstractThe melt mixing technique was used to prepare various polypropylene (PP)‐based (nano)composites. Two commercial organoclays (denoted 20A and 30B) served as the fillers for the PP matrix, and two different maleated (so‐called) compatibilizers (denoted PP‐MA and SMA) were employed as the third component. The results from X‐ray diffraction (XRD) and transmission electron microscope (TEM) experiments revealed that 190 °C was an adequate temperature for preparing the nanocomposites. Nanocomposites were achieved only if specific pairs of organoclay and compatibilizer were simultaneously incorporated in the PP matrix. For example, PP/20A(5 wt %)/PP‐MA(10 wt %) and PP/30B(5 wt %)/SMA(5 wt %) composites exhibited nanoscaled dispersion of 20A or 30B in the PP matrix. Differential scanning calorimetry (DSC) results indicated that the organoclays served as nucleation agents for the PP matrix. Generally, their nucleation effectiveness increased with the addition of compatibilizers. The thermal stability enhancement of PP after adding 20A was confirmed with thermogravimetric analysis (TGA). The enhancement became more evident as a suitable compatibilizer was further added. However, for the 30B‐included composites, thermal stability enhancement was not evident. The dynamic mechanical properties (i.e., storage modulus and loss modulus) of PP increased as the nanocomposites were formed; the properties increment corresponded to the organoclay dispersion status in the matrix. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4139–4150, 2004
Time‐resolved wide‐angle X‐ray scattering measurements during the isothermal crystallization and ferroelectric phase‐transition processes of a vinylidene fluoride/trifluoroethylene copolymer
Authors: Tashiro Kohji , Sasaki Sono , Saragai Seishi 
Published: October 2004

AbstractThe time‐resolved measurement of wide‐angle X‐ray scattering was performed with a synchrotron radiation source during the processes of the isothermal crystallization and ferroelectric phase transition of a vinylidene fluoride/trifluoroethylene copolymer with 73 mol % vinylidene fluoride. When the sample was cooled rapidly from the melt to the temperature region of the paraelectric high‐temperature phase, the peak position of the 200/110 reflection shifted toward the higher angle side and the half‐width became narrower. This indicated an increase in the crystallite size with a more compact chain‐packing mode. Even when the temperature jump was made from the melt into the region of the ferroelectric or low‐temperature phase, the crystallization of the high‐temperature phase was first observed before the appearance of the low‐temperature phase. This was consistent with a prediction based on the so‐called Ostwald state rule: the thermodynamically unstable but kinetically preferable high‐temperature phase can appear first even when the thermodynamically more stable low‐temperature phase should be created. The time‐dependent intensity changes were analyzed with the Avrami kinetic equation. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4175–4181, 2004
Nonisothermal cold‐crystallization kinetics of poly(trimethylene terephthalate)
Authors: Supaphol Pitt , Apiwanthanakorn Nattapol 
Published: October 2004

AbstractThe nonisothermal cold‐crystallization kinetics and subsequent melting behavior of poly(trimethylene terephthalate) (PTT) were investigated with differential scanning calorimetry. The Avrami, Tobin, and Ozawa equations were applied to describe the kinetics of the crystallization process. Both the Avrami and Tobin crystallization rate parameters increased with the heating rate. The Ozawa crystallization rate increased with the temperature. The ability of PTT to crystallize from the glassy state at a unit heating rate was determined with Ziabicki's kinetic crystallizability index, which was found to be about 0.89. The effective energy barrier describing the nonisothermal cold‐crystallization process of PTT was estimated by the differential isoconversional method of Friedman and was found to range between about 114.5 and 158.8 kJ mol−1. In its subsequent melting, PTT exhibited double‐melting behavior for heating rates lower than or equal to 10 °C min−1 and single‐melting behavior for heating rates greater than or equal to 12.5 °C min−1. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4151–4163, 2004