bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix layer sample preparation: An improved MALDI‐MS peptide analysis method for proteomic studies
Authors: Garaguso Ignazio , Borlak Jürgen 
Published: June 2008

AbstractThe analytical performance of MALDI‐MS is highly influenced by sample preparation and the choice of matrix. Here we present an improved MALDI‐MS sample preparation method for peptide mass mapping and peptide analysis, based on the use of the 2,5‐dihydroxybenzoic acid matrix and prestructured sample supports, termed: matrix layer (ML). This sample preparation is easy to use and results in a rapid automated MALDI‐MS and MS/MS with high quality spectra acquisition. The between‐spot variation was investigated using standard peptides and statistical treatment of data confirmed the improvement gained with the ML method. Furthermore, the sample preparation method proved to be highly sensitive, in the lower‐attomole range for peptides, and we improved the performance of MALDI‐MS/MS for characterization of phosphopeptides as well. The method is versatile for the routine analysis of in‐gel tryptic digests thereby allowing for an improved protein sequence coverage. Furthermore, reliable protein identification can be achieved without the need of desalting sample preparation. We demonstrate the performance and the robustness of our method using commercially available reference proteins and automated MS and MS/MS analyses of in‐gel digests from lung tissue lysate proteins separated by 2‐DE.
Genetic or chemical protease inhibition causes significant changes in the Bacillus subtilis exoproteome
Authors: Westers Lidia , Westers Helga , Zanen Geeske , Antelmann Haike , Hecker Michael , Noone David , Devine Kevin M. , van Dijl Jan Maarten , Quax Wim J. 
Published: June 2008

AbstractBacillus subtilis is a prolific producer of enzymes and biopharmaceuticals. However, the susceptibility of heterologous proteins to degradation by (extracellular) proteases is a major limitation for use of B. subtilis as a protein cell factory. An increase in protein production levels has previously been achieved by using either protease‐deficient strains or addition of protease inhibitors to B. subtilis cultures. Notably, the effects of genetic and chemical inhibition of proteases have thus far not been compared in a systematic way. In the present studies, we therefore compared the exoproteomes of cells in which extracellular proteases were genetically or chemically inactivated. The results show substantial differences in the relative abundance of various extracellular proteins. Furthermore, a comparison of the effects of genetic and/or chemical protease inhibition on the stress response triggered by (over) production of secreted proteins showed that chemical protease inhibition provoked a genuine secretion stress response. From a physiological point of view, this suggests that the deletion of protease genes is a better way to prevent product degradation than the use of protease inhibitors. Importantly however, studies with human interleukin‐3 show that chemical protease inhibition can result in improved production of protease‐sensitive secreted proteins even in mutant strains lacking eight extracellular proteases.
Steric effect in alkylation reactions by N‐alkyl‐N‐nitrosoureas: a kinetic approach
Authors: Manso J. A. , Pérez‐Prior M. T. , García‐Santos M. P. , Calle E. , Casado J. 
Published: June 2008

AbstractThe alkylation reactions of 4‐(p‐nitrobenzyl)pyridine (NBP), a trap for alkylating agents with nucleophilic characteristics similar to DNA bases, by five N‐alkyl‐N‐nitrosoureas (methyl‐, ethyl‐, propyl‐, butyl‐, and allylnitrosourea) were investigated in 7:3 (v/v) water/dioxane medium in the 5.0–6.5 pH range. Decomposition of alkylnitrosoureas (ANU) gives rise to alkyldiazonium ions that yield NBP‐R adducts directly or through carbocations in certain instances. The NBP alkylation rate constants by these species were determined. The following sequence of alkylating potential was found: methyl‐ > ethyl‐ > allyl‐ > propyl‐ > butyl group. Application of Ingold–Taft correlation analysis to the kinetic results revealed that the NBP alkylation reactions occur mainly through steric control. The values of the molar absorption coefficients of the NBP‐R adducts also reveal the determinant influence of a steric effect in the formation of alkylation adducts. The kinetic results are consistent with the biological activity of ANU. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetics and mechanism of oxidation of apple pectin by CrVI in aqueous acid medium
Authors: Bellú Sebastián E. , González Juan C. , García Silvia I. , Signorella Sandra R. , Sala Luis F. 
Published: June 2008

AbstractSelective oxidation of galacturonic acid residues of apple pectin by CrVI affords CO2/HCO2H, oxidized pectin, and CrIII as final redox products. The reaction shows first‐order kinetics in [pectin], [CrVI], and [H+], at fixed ionic strength and temperature. Kinetic studies show that the redox reaction proceeds through a mechanism combining CrVI → CrIV → CrII and CrVI → CrIV → CrIII pathways. The mechanism is supported by the observation of free radicals, CrO (the formation of which implies involvement of CrII and CrIV) and CrV (formed in monoelectronic redox processes) as reaction intermediates. The reduction of CrIV and CrV by pectin was independently studied and found to occur more than 103 times faster than pectin + CrVI reaction, in acid medium. At pH 3–5, apple pectin + CrVI redox reaction is slow, oxo‐chromate(V)–pectin species stabilize and remain in solution during several hours. The present results show that these abundant and ubiquitous components of the cell walls of all land plants are able to reduce CrIV–VI or stabilize high‐valent chromium depending on pH. Copyright © 2008 John Wiley & Sons, Ltd.
Hydrogen bond‐directed self‐assembly of peripherally modified cyclotriphosphazenes with a homeotropic liquid crystalline phase
Authors: Xu Jianwei , Ling Toh Cher , He Chaobin 
Published: June 2008

AbstractThe synthesis and characterization of hydrogen‐bonded star‐shaped complexes consisting of stilbazolyloxy, azopyridyl, and Schiff base‐substituted cyclotriphosphazenes (3a, 3b, and 3c, respectively) and monoalkyloxy, bis(dodecyloxy), and tris(dodecyloxy)benzoic acids are reported. The thermal behaviors of complexes are studied by the means of differential scanning calorimetry, polarizing optical microscopy, and X‐ray diffractometry. Only 3a and 3b with monoalkyloxybenzoic acids show a homeotropic smectic A mesophase. The effect of azo and ethylene linkage of mesogenic groups in the cyclotriphosphazenes and the length of the flexible chain in monoalkyloxybenzoic acids on mesophase transition behaviors are investigated, revealing that the linkages in mesogenic groups governs the phase transition temperatures, and the length of flexible chain in proton donors plays an important role in controlling the magnitude of enthalpy and entropy of mesophase transitions in this supramolecular liquid crystal system. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4691–4703, 2008
Thermally enhanced photoinduced in‐plane reorientation in photo‐cross‐linkable polymer liquid crystalline films and its application to linear polarizer
Authors: Kawatsuki Nobuhiro , Tsutsumi Ryoji , Hiraiwa Akie , Takatsuka Hirofumi , Sakai Takeya 
Published: June 2008

AbstractThermally enhanced photoinduced in‐plane molecular reorientation in new photo‐cross‐linkable polymer liquid crystalline (PPLC) films comprising 4‐[ω‐(4‐methoxycinnamoyloxy)alkyloxy]biphenyl side groups is explored using linearly polarized ultraviolet (LPUV) light exposure and subsequent annealing. The influence of the alkylene spacer length between the photo‐cross‐linkable group and the biphenyl mesogenic moiety is investigated. The straight‐line characteristics of the photoreactive mesogenic side group and the 4‐methoxycinnamoyl group play important roles in the high photoreactivity and the large thermally enhanced molecular reorientation, where the in‐plane order and the birefringence of the reoriented film are 0.61 and 0.18 are obtained. Finally, cooperative molecular reorientation of dichroic dyes doped in PPLC films is also achieved to fabricate a linear polarizer. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4712–4718, 2008
Copolymerization of ethylene with cyclopentene or 2‐butene with half titanocenes‐based catalysts
Authors: Napoli Mariagrazia , Mariconda Annaluisa , Immediata Ivano , Longo Pasquale 
Published: June 2008

AbstractHalf titanocenes (CpCH2CH2O)TiCl2 (1), (CpCH2CH2OCH3)TiCl3 (2), and CpTiCl3 (3), activated by methylaluminoxane (MAO) were tested in copolymerization of ethylene with internal olefins such as cyclopentene. All the catalysts were able to give incorporation of cyclopentene in polyethylene matrix. 13C NMR analysis of obtained copolymers showed that the catalytic systems have low regiospecificity. In fact, in ethylene–cyclopentene copolymers, cyclic olefin inserts with both 1,2 and 1,3‐enchainment. X‐ray powder diffraction analysis of these copolymers confirmed that 1,2 inserted cyclopentene units are excluded from crystalline phase, whereas 1,3‐cyclopentene units are included, giving rise to expansion of unit cell of crystalline polyethylene. Titanium‐based catalysts were investigated also in the copolymerization of ethylene with E and Z‐2‐butene. Only complex (1) was able to give copolymers and 13C NMR analysis of products showed 2‐3, 1‐3, and 1‐2 insertion of 2‐butene. Differential scanning calorimetry analysis displayed that ethylene–cyclopentene, as well as ethylene‐2‐butene, copolymers are crystalline and their melting point decreases by increasing the comonomer content. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4725–4733, 2008
Preparation of polysulfone‐g‐poly(N‐isopropylacrylamide) graft copolymers through atom transfer radical polymerization and formation of temperature‐responsive nanoparticles
Authors: Liu Ying‐Ling , Lin Guo‐Chain , Wu Chuan‐Shao 
Published: June 2008

AbstractPolysulfone‐g‐poly(N‐isopropylacrylamide) (PSf‐g‐PNIPAAm) graft copolymers were prepared from atom transfer radical polymerization of NIPAAm using chloromethylated PSf as a macro‐initiator. The chain lengths of PNIPAAm of the graft copolymers were controllable with polymerization reaction time. The chemical structures of the graft copolymers were characterized with FTIR, NMR, and elemental analysis and their amphiphilic characteristics were examined and discussed. The PSf‐g‐PNIPAAm graft copolymers and the nanoparticles made from the graft copolymers exhibited repeatable temperature‐responsive properties in heating–cooling cycles. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4756–4765, 2008
Grafting of polyamide 6 by the anionic polymerization of ε‐caprolactam from an isocyanate bearing polystyrene backbone
Authors: Zhang Cai‐Liang , Feng Lian‐Fang , Hoppe Sandrine , Hu Guo‐Hua 
Published: June 2008

AbstractThe grafting of polyamide 6 (PA6) onto polystyrene (PS) can rely on the use of a copolymer of styrene (St) and 3‐isopropenyl‐α, α‐dimethylbenzene isocyanate (TMI), PS‐co‐TMI, to activate the polymerization of ε‐caprolactam (CL) in the presence of sodium ε‐caprolactam (NaCL) as an anionic catalyst. This article is aimed at answering the following key questions. First, do all the isocyanate moieties of the PS‐co‐TMI participate in the activation of the polymerization of CL? Second, what are the composition of the resulting polymer product and the structure of the resulting graft copolymer? The results show that the isocyanate moieties had all participated in the activation of the polymerization, implying that each isocyanate moiety has led to the formation of a PA6 graft. The as‐polymerized product was composed of a pure PS‐g‐PA6 graft copolymer, homo‐PA6, and unreacted CL. Moreover, when the composition of a PS‐co‐TMI/CL/NaCL system was fixed, the mass ratio between the PA6 grafts and PS backbone of the pure PS‐g‐PA6 graft copolymer was almost a constant and was almost independent of its molar mass. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4766–4776, 2008
Cationic polymerizations of 2‐alkyloxazolines catalyzed by bismuth salts
Authors: Buzin Pavel , Schwarz Gert , Kricheldorf Hans R. 
Published: June 2008

AbstractAcidic bismuth salts, such as BiCl3, BiBr3, BiJ3, and Bi‐triflate catalyzed the ring‐opening polymerization of 2‐methoxazoline (MOZ) in bulk at 100 °C, whereas less acidic salts such as Bi2O3 or Bi(III)acetate did not. Bi‐triflate‐catalyzed polymerizations of 2‐ethyloxazoline (EtOZ) were performed with variation of the monomer–catalyst ratio (M/C). It was found that the molecular weights were independent of the M/C ratio. The formation of cationic chain ends and the absence of cycles was proven by reactions of virgin polymerization products with N,N‐dimethyl‐4‐aminopyridine or triphenylphosphine. The resulting polymers having modified cationic chain ends were characterized by 1H NMR spectroscopy and MALDI‐TOF mass spectrometry. The polymerization mechanism including chain‐transfer reactions is discussed. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4777–4784, 2008
Initiator effect on the cationic ring‐opening copolymerization of 2‐ethyl‐2‐oxazoline and 2‐phenyl‐2‐oxazoline
Authors: Fijten Martin W. M. , Hoogenboom Richard , Schubert Ulrich S. 
Published: June 2008

AbstractThe aim of this research was to study the effect of the initiator on the resulting monomer distribution for the cationic ring‐opening copolymerization of 2‐ethyl‐2‐oxazoline (EtOx) and 2‐phenyl‐2‐oxazoline (PhOx). At first, kinetic studies were performed for the homopolymerizations of both monomers at 160 °C under microwave irradiation using four initiators. These initiators have the same benzyl‐initiating group but different leaving groups, Cl−, Br−, I−, and OTs−. The basicity of the leaving group affects the ratio of covalent and cationic propagating species and, thus, the polymerization rate. The observed differences in polymerization rates could be correlated to the concentration of cationic species in the polymerization mixture as determined by 1H NMR spectroscopy. In a next‐step, polymerization kinetics were determined for the copolymerizations of EtOx and PhOx with these four initiators. The reactivity ratios for these copolymerizations were calculated from the polymerization rates obtained for the copolymerizations. This approach allows more accurate determination of the copolymerization parameters compared to conventional methods using the composition of single polymers. When benzyl chloride (BCl) was used as an initiator, no copolymers could be obtained because its reactivity is too low for the polymerization of PhOx. With decreasing basicity of the used counterions (Br− > I− > OTs−), the reactivity ratios gradually changed from rEtOx = 10.1 and rPhOx = 0.30 to rEtOx = 7.9 and rPhOx = 0.18. However, the large difference in reactivity ratios will lead to the formation of quasi‐diblock copolymers in all cases. In conclusion, the used initiator does influence the monomer distribution in the copolymers, but for the investigated system the differences were so small that no difference in the resulting polymer properties is expected. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4804–4816, 2008
Pathologic stage T2a and T2b prostate cancer in the recent prostate‐specific antigen era: Implications for unilateral ablative therapy
Authors: Polascik Thomas J. , Mayes Janice M. , Sun Leon , Madden John F. , Moul Judd W. , Mouraviev Vladimir 
Published: June 2008

AbstractBACKGROUNDEarly detection of small volume prostate cancer (PCa) has led to the concept of focal therapy to treat in an organ‐sparing manner. We evaluated trends in pathologic staging among patients with localized PCa undergoing radical prostatectomy (RP), defining the frequency of unilateral cancers during 1988–1995, 1996–2000 and 2001–2006.METHODSData were abstracted from the Duke Prostate Cancer Outcome database selecting 3,676 men with available pathology treated with RP. Based on surgical pathology, trends in as pathological T (pT) stage, pathological Gleason Score (pGS), and percent tumor involvement (PTI) were evaluated.RESULTSpT2a increased from 2.8% of men undergoing RP in 1988–1995 to 13.0% during 2001–2006 (P  <  0.0005). PTI analysis shifted towards low volume disease, e.g. PTI ≤ 5% increased from 10% during 1988–1995, to 37% in 2001–2006 (P < 0.005). Of all pT2a disease throughout 1988–2006, an increase in proportion of pT2a tumors from 10% during 1988–1995 to 69.4% during 2001–2006 was identified. Over three eras, pT2a had minimal (65% had PTI ≤ 5%) or small volume (14% had PTI 5.01–10.00) disease, and 59% were low grade (pGS ≤ 6). Using a Cox Hazard model, pT2a versus pT2b disease, surgical margins, PTI, and PSA statistically contributed to PSA disease‐free survival in the contemporary era 2001–2006.CONCLUSIONSThe increasing prevalence of unilateral pT2a/T2b PCa characterizes a growing proportion of men recently electing RP. These tumors are associated with lower PTI, pGS ≤ 7, and demonstrated better PSA‐free survival in the 2001–2006 era. These low risk pathologic characteristics may allow for unilateral focal therapy in carefully selected patients. Prostate 68: 1380–1386, 2008. © 2008 Wiley‐Liss, Inc.
GOLPH2 and MYO6: Putative prostate cancer markers localized to the Golgi apparatus
Authors: Wei Shuanzeng , Dunn Thomas A. , Isaacs William B. , De Marzo Angelo M. , Luo Jun 
Published: June 2008

AbstractBACKGROUNDMalignant transformation is often accompanied by morphological and functional alterations in subcellular organelles. The Golgi apparatus is a subcellular structure primarily involved in modification and sorting of macromolecules for secretion and transport to other cellular destinations. Molecular alterations associated with the Golgi apparatus may take place during prostate carcinogenesis but such alterations have not been documented.METHODSTo demonstrate that the Golgi apparatus undergoes alterations during prostate carcinogenesis, we examined the expression and localization of two candidate molecules, Golgi phosphoprotein 2 (GOLPH2) and myosin VI (MYO6), both overexpressed in prostate cancer as initially identified by expression microarray analysis.RESULTSElevated GOLPH2 expression in prostate cancers was validated through real‐time RT‐PCR, Western blot, and tissue microarray analysis, and its Golgi localization in surgical prostate cancer tissues confirmed using two‐color immunofluorescence. In addition, distinctive juxtanuclear MYO6 staining pattern consistent with Golgi localization was observed in surgical prostate cancer tissues. Two‐color immunofluorescence revealed intensive Golgi‐specific staining for both GOLPH2 and myosin VI in prostate cancer cells but not in the adjacent normal prostate epithelium.CONCLUSIONSWe show that the Golgi apparatus in prostate cancer cells differs from the normal Golgi by elevated levels of two molecules, GOLPH2 and MYO6. These results for the first time demonstrated consistent cancer cell‐specific alterations in the molecular composition of the Golgi apparatus. Such alterations can be explored for discovery of novel prostate cancer biomarkers through targeted organellar approaches. Prostate 68: 1387–1395, 2008. © 2008 Wiley‐Liss, Inc.
X‐ray structure of ILL2, an auxin‐conjugate amidohydrolase from Arabidopsis thaliana
Authors: Bitto Eduard , Bingman Craig A. , Bittova Lenka , Houston Norma L. , Boston Rebecca S. , Fox Brian G. , Phillips George N. 
Published: June 2008

AbstractThe plant hormone indole‐3‐acetic acid (IAA) is the most abundant natural auxin involved in many aspects of plant development and growth. The IAA levels in plants are modulated by a specific group of amidohydrolases from the peptidase M20D family that release the active hormone from its conjugated storage forms. Here, we describe the X‐ray crystal structure of IAA‐amino acid hydrolase IAA‐leucine resistantlike gene 2 (ILL2) from Arabidopsis thaliana at 2.0 Å resolution. ILL2 preferentially hydrolyses the auxin‐amino acid conjugate N‐(indol‐3‐acetyl)‐alanine. The overall structure of ILL2 is reminiscent of dinuclear metallopeptidases from the M20 peptidase family. The structure consists of two domains, a larger catalytic domain with three‐layer αβα sandwich architecture and aminopeptidase topology and a smaller satellite domain with two‐layer αβ‐sandwich architecture and α–β‐plaits topology. The metal‐coordinating residues in the active site of ILL2 include a conserved cysteine that clearly distinguishes this protein from previously structurally characterized members of the M20 peptidase family. Modeling of N‐(indol‐3‐acetyl)‐alanine into the active site of ILL2 suggests that Leu175 serves as a key determinant for the amino acid side‐chain specificity of this enzyme. Furthermore, a hydrophobic pocket nearby the catalytic dimetal center likely recognizes the indolyl moiety of the substrate. Finally, the active site of ILL2 harbors an absolutely conserved glutamate (Glu172), which is well positioned to act as a general acid‐base residue. Overall, the structure of ILL2 suggests that this enzyme likely uses a catalytic mechanism that follows the paradigm established for the other enzymes of the M20 peptidase family. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Vibrational properties in nanocrystalline nickels: temperature effects and composite model for thermodynamics
Authors: Tang Jian‐Feng , Li Xue‐Song , Long Wo‐Yun , Wang Yong 
Published: June 2008

AbstractBased on the atomic local structure, a nanocrystalline material is separated into two parts: inner grains and grain boundaries. Molecular dynamics simulations have been performed to study the difference in their vibrational properties in nanocrystalline nickels. The results obtained reveal that a similar phonon frequency softening as in the perfect lattice mainly focuses on grains in nanocrystalline materials, and for the grain boundary part there is no obvious change in the vibrational density of states in the temperature range 300–900 K, especially in the lower frequency range. Comparing with conventional crystals, the higher specific heat and vibrational entropy, and lower vibrational free energy with decreasing mean grain size, result from the high proportion of grain boundaries in nanocrystals. In addition, the composite model provides a good description of the contributions of grain and grain boundary phases to thermodynamic quantities. Supposing the nanocrystalline material can be treated as a composite composed of grain and grain boundary network, the vibrational thermodynamic quantities of the system can be well determined from the proportion of grain boundaries and the corresponding thermodynamic quantities of grain and grain boundary parts. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of temperature on the magnetic properties of Fe3O4 thin films studied by ferromagnetic resonance (FMR)
Authors: Budak S. , Yildiz F. , Ozdemir M. , Aktas B. 
Published: June 2008

AbstractSingle crystalline Fe3O4 thin films of 110 Å thickness grown on MgO (100) substrate have been investigated by Ferromagnetic Resonance (FMR) technique as a function of temperature between 3 and 300 K. A strong unidirectional (exchange) anisotropy field was detected as evidence from a shift of the resonance field for the r‐FC case relative to that for n‐FC case at lower temperature. Using a field‐induced unidirectional exchange and bulk anisotropy, with the usual magneto‐crystalline cubic anisotropy energy, we have simulated both the experimental spectra and angular dependence of resonance field to deduce anisotropy and other magnetic parameters as a function of temperature. Magnetic parameters and Verwey transition for the thin film case were found to shift down to around 90 K from 120 K for bulk sample of the same compound as well. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)