bluuebunny/crossref_metadata_2025 huggingface dataset:
Using protein/creatinine ratios in random urine
Authors: Watanabe Mitsuhiro , Funabiki Kazuhiko , Tsuge Toshinao , Maeda Kunimi , Horikoshi Satoshi , Tomino Yasuhiko
Published: July 2005

We assessed the new test paper Multistix PRO IOLS, in which the ±region of the conventional test for protein was altered so that creatinine correction became possible. Urinary samples from 235 patients with various renal diseases were obtained from the Juntendo University Hospital. We examined 1) the correlation between qualitatively measured values of urinary protein by the new test paper and the conventional test paper, and 2) the correlation between qualitative and quantitative values of protein (P), creatinine (C), and the P/C ratio measured by the new test paper. There was a good correlation between the P/C ratio observed with the new test paper and that observed by quantitative analysis. There was also a good correlation of the P/C ratio between 24‐hr urine and urinary samples obtained at any time of day. Thus, it appears that the results obtained from urinary samples any time of day can predict the amount of protein excreted during the day. J. Clin. Lab. Anal. 19:160–166, 2005. © 2005 Wiley‐Liss, Inc.
The non‐proteolytically active thrombin peptide TP508 stimulates angiogenic sprouting
Authors: Vartanian Keri B. , Chen Helen Y.S. , Kennedy Janelle , Beck Shaleen K. , Ryaby James T. , Wang Hali , Hoying James B.
Published: July 2005

Thrombin is a serine protease that promotes platelet aggregation, blood coagulation, and tissue repair. A peptide derived from a non‐proteolytically active region of thrombin, TP508, also promotes tissue repair and increased vascularity, yet does not activate platelet and inflammatory cascades. TP508 binds to cells with high affinity and stimulates cells independent of the proteolytically active thrombin receptors (PARs) and thus is considered to activate a non‐proteolytically active receptor (non‐PAR) pathway. Using a model of angiogenic sprouting, we further defined the angiogenic potential of TP508 and investigated the role of non‐proteolytic, thrombin‐mediated pathways in angiogenesis. The assay involves measuring angiogenic sprouting from cultured, intact microvessel fragments. In this assay, TP508 stimulated angiogenic sprouting to an extent similar to or greater than the potent angiogenic factor, VEGF. However, TP508 had no significant effect on the number of sprouts that formed per vessel. In contrast to TP508, proteolytically active receptor agonists had no effect or inhibited angiogenic sprouting. The increased sprouting activity stimulated by TP508 was VEGF dependent but did not involve an increase in VEGF mRNA expression above baseline levels. These results suggest that TP508 acts early in angiogenesis and directly on microvascular cells to accelerate sprouting, but not to induce more sprouting, in a manner different than the intact thrombin molecule. © 2005 Wiley‐Liss, Inc.
CCL18‐stimulated upregulation of collagen production in lung fibroblasts requires Sp1 signaling and basal Smad3 activity
Authors: Luzina Irina G. , Tsymbalyuk Natalya , Choi Jung , Hasday Jeffrey D. , Atamas Sergei P.
Published: July 2005

A CC chemokine CCL18 stimulates collagen production in pulmonary fibroblasts through an unknown signaling mechanism. In this study, involvement of Sp1 and Smad3 in CCL18 signaling in primary human pulmonary fibroblast cultures was investigated. Phosphorylation of Sp1, DNA‐binding by Sp1, and the activity of an Sp1‐dependent reporter were all increased in response to CCL18 stimulation. CCL18 did not stimulate a detectable increase in Smad3 phosphorylation or Smad3/4 DNA‐binding activity, although some basal phosphorylation and DNA binding by Smad3/4 were noted. Transient overexpression of dominant negative mutants of Sp1 and Smad3 abrogated CCL18‐dependent upregulation as well as basal production of collagen. These observations suggested that CCL18 activates collagen production in pulmonary fibroblasts through an Sp1‐dependent pathway that also requires basal Smad3 activity. Possible involvement of autocrine TGF‐β in CCL18 signaling was considered. CCL18 stimulated increases in collagen mRNA and protein production without detectable changes in TGF‐β1, ‐β2, and ‐β3 mRNA or protein levels. Neutralizing anti‐TGF‐β antibodies, latency‐associated peptide, ALK5‐specific inhibitor SD431542, and an inhibitor of the protease‐dependent TGF‐β activation aprotinin, each failed to block CCL18‐stimulated collagen production. These observations suggest that both CCL18 signaling in pulmonary fibroblasts and basal Smad3 activity are independent of autocrine TGF‐β. © 2005 Wiley‐Liss, Inc.
Trypsin and thrombin accelerate aggregation of human endocrine pancreas precursor cells
Authors: Wei Chiju , Geras‐Raaka Elizabeth , Marcus‐Samuels Bernice , Oron Yoram , Gershengorn Marvin C.
Published: July 2005

Human islet‐derived precursor cells (hIPCs) and human pancreatic ductal carcinoma (PANC‐1) cells can be induced to form aggregates that subsequently differentiate into hormone‐expressing islet‐like cell aggregates (ICAs). We show that challenge of hIPCs or PANC‐1 cells with thrombin or trypsin resulted in stimulation of signaling via the inositol‐tris‐phosphate second messenger pathway leading to rapid, transient increases in cytosolic calcium ion concentration in the majority of the cells. Because we found that hIPCs, PANC‐1 cells, human fetal pancreas, and human adult islets express two protease‐activated receptors (PARs), PAR‐1 and PAR‐2, we tested whether the effects of thrombin and trypsin were mediated, at least in part, by these receptors. Peptide agonists that are relatively specific for PAR‐1 (SFLLRN‐amide) or PAR‐2 (SLIGRL‐amide) stimulated increases in inositol phosphates and cytosolic calcium ion concentration, and increased the phosphorylation of Rho, a small G‐protein associated with cytoskeletal changes affecting cellular morphology and migration. Most importantly, we show that these agonists increased the rate of hIPC aggregation leading to the formation of more viable, smaller ICAs. Our data show that thrombin and trypsin accelerate aggregation, an early stage of hIPC differentiation in vitro, and imply that pancreatic trypsin and thrombin may be involved in islet development in vivo. J. Cell. Physiol. 206: 322–328, 2006. Published 2005 Wiley‐Liss, Inc.
3,5,3′‐triiodothyronine (T3) is a survival factor for pancreatic β‐cells undergoing apoptosis
Authors: Verga Falzacappa Cecilia , Panacchia Laura , Bucci Barbara , Stigliano Antonio , Cavallo Maria Gisella , Brunetti Ercole , Toscano Vincenzo , Misiti Silvia
Published: July 2005

3,5,3′‐triiodothyronine (T3) is essential for the growth and the regulation of metabolic functions, moreover, the growth‐stimulatory effect of T3 has largely been demonstrated and the pathways via which T3 promotes cell growth have been recently investigated. Type 1 diabetes (T1D) is due to the destruction of β‐cells, which occurs even through apoptosis. Aim of our study was to analyze whether T3 could have an antiapoptotic effect on cultured β‐cells undergoing apoptosis. We have demonstrated that T3 promotes cell proliferation in islet β‐cell lines (rRINm5F and hCM) provoking an increment in cell number (up to 55%: rRINm5F and 45%: hCM), cell viability, and BrdU incorporation, and regulating the cell cycle‐related molecules (cyc A, D1, E, and p27kip1). T3 inhibited the apoptotic process induced by streptozocin, S‐Nitroso‐N‐Acetylpenicylamine (SNAP), and H2O2 via regulation of the pro‐ and anti‐apoptotic factors Bcl‐2, Bcl‐XL, Bad, Bax, and Caspase 3. The T3 protective effect was PI‐3 K‐, but not MAPK‐ or PKA‐mediated, involving pAktThr308. Thus, T3 could be considered a survival factor protecting islet β‐cells from apoptosis. J. Cell. Physiol. 206: 309–321, 2006. © 2005 Wiley‐Liss, Inc.
Measurements of the kinetics of the OH‐initiated oxidation of β‐pinene: Radical propagation in the OH + β‐pinene + O2 + NO reaction system
Authors: Davis Maxine E. , Tapscott Craig , Stevens Philip S.
Published: July 2005

The mechanism of the OH‐initiated oxidation of β‐pinene in the presence of NO has been investigated using a discharge‐flow system at 5 Torr and 300 K. OH radical concentrations were measured as a function of reaction time by laser‐induced fluorescence (LIF). The rate constant for the OH +β‐pinene reaction was measured to be (7.68 ± 0.72) ×10−11 cm3 molecule−1 s−1. OH radical propagation was observed after the addition of O2 and NO, and the measured OH concentration profiles were compared to simulations based on both the Master Chemical Mechanism and the Regional Atmospheric Chemistry Mechanism for β‐pinene oxidation in order to determine the ability of these mechanisms to describe the observed efficiency of radical propagation. Both models are able to reproduce the observed OH concentrations profiles to within 15%. Expanding the MCM to include isomerization of the β‐hydroxy alkoxy radicals improves the agreement with the experimental observations. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 522–531, 2005
Comparative sensitivity analysis of transport properties and reaction rate coefficients
Authors: Brown Nancy J. , Revzan Kenneth L.
Published: July 2005

Transport properties of chemical species are required for many combustion models. A sensitivity analysis is conducted to assess the significance of transport properties and their underlying molecular parameterizations for atmospheric pressure premixed laminar flames for three different fuels and two different approaches to transport property calculations. The analysis is performed at both the macroscopic level of Arrhenius A‐factors and transport coefficients as well as at the molecular scale. First‐ and second‐order sensitivities of reactant, intermediate, and product species concentrations, temperature, and flame velocity were calculated with respect to various parameters, all within the mixture approximation using ADIFOR 2.0, a software package that supports exact differentiation. Parameters considered were the binary diffusion coefficients, pure species thermal conductivity coefficients, and thermal diffusion ratios. The more fundamental molecular parameters: collision diameters, well depths, dipole moments, polarizabilities, and the rotational relaxation collision numbers were also considered.

Influential transport properties are found to be as important in flame modeling as influential reaction rates, and both should be taken into account when building chemical mechanisms. Transport parameter importance was found to vary according to the independent variable being considered and the flame type. Magnitudes of sensitivities appear to be more influenced by the underlying molecular parameters than the approach used to compute the transport properties. The number of significant sensitivities to transport parameters increases for the progression: flame temperature, flame velocity, reactant species, product species, and intermediate radical species. Many dependent variables have significant sensitivities to the pure species thermal conductivities of N2, O2, and the fuel. At the molecular level, large sensitivities to the collision diameters of several species are also observed, but significant sensitivity to well depths, although observed is less and more rare. Large sensitivities are not observed to the rotational relaxation collision number, the dipole moment, or to the molecular polarizability. Second‐order sensitivities are significant for a number of dependent variables. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 538–553, 2005
Boronolectins and fluorescent boronolectins: An examination of the detailed chemistry issues important for the design
Authors: Yan Jun , Fang Hao , Wang Binghe
Published: July 2005

Glycans in the form of glycoproteins or glycolipids play very critical roles in various biological and pathological processes including inflammation, cancer metastasis, immune reactions, embryo development, cell–cell communications and adhesions, blood generation, etc. Proteins (lectins) that can recognize carbohydrates have played very important roles in studying glycobiology. Small molecule mimics of lectins will be very useful in the development of new therapeutics and diagnostics. Along this line, boronic acids have been widely used in the design and synthesis of small organic compounds that mimic the function of lectins. This review examines in detail the factors that are important for the design of boronic acid‐based lectin mimics, boronolectins. © 2005 Wiley Periodicals, Inc.
Fatigue of muscles weakened by death of motoneurons
Authors: Thomas Christine K. , Zijdewind Inge
Published: July 2005

Weakness is a characteristic of muscles influenced by the postpolio syndrome (PPS), amyotrophic lateral sclerosis (ALS), and spinal cord injury (SCI). The strength deficits relate to changes in muscle use and to the chronic denervation that can follow the spinal motoneuron death common to these disorders. PPS, ALS, and SCI also involve variable amounts of supraspinal neuron death, the effects of which on muscle weakness remains unclear. Nevertheless, weakness of muscle itself defines the functional consequences of these disorders. A weaker muscle requires an individual to work that muscle at higher than usual intensities relative to its maximal capacity, inducing progressive fatigue and an increased sense of effort. Little evidence is available to suggest that the fatigue commonly experienced by individuals with these disorders relates to an increase in the intrinsic fatigability of the muscle fibers. The only exception is when SCI induces chronic muscle paralysis. To reduce long‐term functional deficits in these disorders, studies must identify the signaling pathways that influence neuron survival and determine the factors that encourage and limit sprouting of motor axons. This may ensure that a greater proportion of the fibers in each muscle remain innervated and available for use. Muscle Nerve, 2005
Modeling multiple stage manufacturing systems with generalized costs and capacity issues
Authors: Simpson N.C. , Erenguc S. Selcuk
Published: July 2005

This study introduces one modeling methodology that describes a broad range of multiple stage production planning issues, including multiple limited resources with setup times and joint fixed cost relationships. An existing production system is modeled in this fashion, creating a new set of 1350 highly generalized benchmark problems. A computational study is conducted with the 1350 benchmark problems introduced in this paper and 2100 benchmark problems, with more restrictive assumptions, from the existing literature. The relative merits of a decomposition‐based algorithm and a neighborhood search technique known as NIPPA, or the Non‐sequential Incremental Part Period Algorithm, are assessed. NIPPA is generally the more successful of the two techniques, although there are specific instances in which the decomposition‐based algorithm displayed a distinct advantage. © 2005 Wiley Periodicals, Inc. Naval Research Logistics, 2005
Properties of the geometric and related processes
Authors: Braun W. John , Li Wei , Zhao Yiqiang Q.
Published: July 2005

Some properties of the geometric process are studied along with those of a related process which we propose to call the α‐series process. It is shown that the expected number of counts at an arbitrary time does not exist for the decreasing geometric process. The decreasing version of the α‐series process does have a finite expected number of counts, under certain conditions. This process also has the same advantages of tractability as the geometric process; it exhibits some properties which may make it a useful complement to the increasing geometric process. In addition, it may be fit to observed data as easily as the geometric process. Applications in reliability and stochastic scheduling are considered in order to demonstrate the versatility of the alternative model. © 2005 Wiley Periodicals, Inc. Naval Research Logistics, 2005
Machine scheduling with pickup and delivery
Authors: Li Chung‐Lun , Ou Jinwen
Published: July 2005

The coordination of production, supply, and distribution is an important issue in logistics and operations management. This paper develops and analyzes a single‐machine scheduling model that incorporates the scheduling of jobs and the pickup and delivery arrangements of the materials and finished jobs. In this model, there is a capacitated pickup and delivery vehicle that travels between the machine and the storage area, and the objective is to minimize the makespan of the schedule. The problem is strongly NP‐hard in general but is solvable in polynomial time when the job processing sequence is predetermined. An efficient heuristic is developed for the general problem. The effectiveness of the heuristic is studied both analytically and computationally. © 2005 Wiley Periodicals, Inc. Naval Research Logistics, 2005.
Boundary element‐free method (BEFM) for two‐dimensional elastodynamic analysis using Laplace transform
Authors: Liew K. M. , Cheng Yumin , Kitipornchai S.
Published: July 2005

In this paper, we present a direct meshless method of boundary integral equation (BIE), known as the boundary element‐free method (BEFM), for two‐dimensional (2D) elastodynamic problems that combines the BIE method for 2D elastodynamics in the Laplace‐transformed domain and the improved moving least‐squares (IMLS) approximation. The formulae for the BEFM for 2D elastodynamic problems are given, and the numerical procedures are also shown. The BEFM is a direct numerical method, in which the basic unknown quantities are the real solutions of the nodal variables, and the boundary conditions can be implemented directly and easily that leads to a greater computational precision. For the purpose of demonstration, some selected numerical examples are solved using the BEFM. Copyright © 2005 John Wiley & Sons, Ltd.
Up‐regulation of cathepsin X in Helicobacter pylori gastritis and gastric cancer
Authors: Krueger Sabine , Kalinski Thomas , Hundertmark Tanja , Wex Thomas , Küster Dörthe , Peitz Ulrich , Ebert Matthias , Nägler Dorit K , Kellner Udo , Malfertheiner Peter , Naumann Michael , Röcken Christoph , Roessner Albert
Published: July 2005

Recently, we identified increased cathepsin X expression in H. pylori‐infected gastric mucosa. Here, we describe further up‐regulation in gastric cancer and report on the role of inflammatory cytokines required for cathepsin X up‐regulation in H. pylori‐infected gastric mucosa, as well as on consequences for cellular invasion. Biopsy specimens were taken from the antrum, corpus and cardia of H. pylori‐infected and non‐infected patients. Gastric cancer samples were obtained from patients undergoing gastric surgery. Cathepsin X was detected in gastric mucosa by quantitative real‐time RT‐PCR, western blotting and immunohistochemistry. Induction of cathepsin X expression in epithelial and inflammatory cells caused by H. pylori infection was tested in in vitro contact and non‐contact co‐cultures of AGS cells and monocytic cells. Patients with H. pylori gastritis showed significantly higher cathepsin X mRNA (2.5‐fold) and protein (1.6‐fold) expression than H. pylori‐negative patients. Cathepsin X was also up‐regulated in gastric cancer (3–12‐fold) compared to non‐neoplastic mucosa. Cathepsin X was predominantly expressed by macrophages in the mucosal stroma and in glands of the antral mucosa. In addition, tumour cells stained for cathepsin X in 26 (68%) patients with gastric carcinoma. In general, staining was significantly more common (20 vs. 6 patients) and more intense (3.55 vs. 0.83) in intestinal type gastric cancer than in the diffuse type. In vitro cell culture experiments revealed that intercellular signalling between pathogenicity island (PAI)‐positive H. pylori‐infected epithelial cells and macrophages via soluble factors in the culture medium seems to be responsible for increased expression of cathepsin X in monocytes. Using antisense oligonucleotides, cathepsin X up‐regulation was directly associated with higher invasiveness in vitro. Although no correlation of cathepsin X expression and TNM stage was found, our study demonstrates that cathepsin X plays a role not only in the chronic inflammation of gastric mucosa but also in the tumourigenesis of gastric cancer. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Amplification of genes encoding KIT, PDGFRα and VEGFR2 receptor tyrosine kinases is frequent in glioblastoma multiforme
Authors: Joensuu Heikki , Puputti Marjut , Sihto Harri , Tynninen Olli , Nupponen Nina N
Published: July 2005

KIT, platelet‐derived growth factor receptors (PDGFRs) and vascular endothelial growth factor receptors (VEGFRs) are important clinical targets for tyrosine kinase inhibitors. The frequency of KIT and VEGFR2 amplification in glioblastomas is not known, and few data are available in any other human tumour type. We investigated 43 primary glioblastomas for KIT, VEGFR2, PDGFRA and EGFR amplification using fluorescence in situ hybridization. KIT was amplified in 47% and VEGFR2 in 39% of the glioblastomas, respectively, and PDGFRA in 29%. Thirty‐five (81%) of the tumours had either KIT or EGFR amplification. KIT, PDGFRA and VEGFR2 amplifications were strongly associated (p < 0.0001 for each pairwise comparison), suggesting co‐amplification, whereas no significant association was found with EGFR amplification. The four secondary glioblastomas arising from pre‐existing lower grade astrocytic tumours investigated had KIT amplification but none had EGFR amplification. No mutations were detected with denaturing high‐performance liquid chromatography in KIT exons 9, 11, 13 or 17, PDGFRA exons 12 and 18, or EGFR exons 18, 19 or 21. Glioblastomas with KIT, PDGFR or VEGFR2 amplification were associated with similar outcome to other glioblastomas. We conclude that KIT, PDGFRA and VEGFR2 are commonly amplified in primary glioblastoma and that they may also be amplified in secondary glioblastoma. Amplified kinases may be potential targets for tyrosine kinase inhibitor therapy. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
In vitro enzymatic degradation kinetics of polymeric blends of crosslinked starch and carboxymethyl cellulose
Authors: Bajpai AK , Shrivastava Jyoti
Published: July 2005

Hydrophilic blend matrices of crosslinked starch and carboxymethyl cellulose were synthesized and their susceptibilities to enzymatic degradation were assessed by taking α‐amylase as a model enzyme. The polymeric blends were characterized by FT‐IR spectroscopy, differential scanning calorimetry and scanning electron microscopy. The influence of the chemical compositions of the blends, and the pH values and temperatures of the α‐amylase solutions was investigated by studying the swelling and degradation kinetics of the blends. The impact of the concentrations of the enzyme solutions on the degradation profiles was also examined. The blends were found to exhibit a mixed type of degradation mechanism, ie both diffusion and surface erosion. Copyright © 2005 Society of Chemical Industry
A simplified 2‐D electrophoresis protocol with the aid of an organic disulfide
Authors: Hedberg Jesper J. , Bjerneld Erik J. , Cetinkaya Siham , Goscinski Jan , Grigorescu Ioana , Haid Daniel , Laurin Ylva , Bjellqvist Bengt
Published: July 2005

2‐DE is still a relatively cumbersome and labor intensive method. Given the successful cysteinyl protection concept with hydroxyethyl disulfide (specific oxidation) during the first dimension separation, the possibility for a simplified equilibration procedure was investigated. This was achieved by maintaining the S‐mercaptoethanol modified cysteinyls throughout the 2‐D workflow including second dimension separation, spot handling, protein digestion, and protein identification. The traditional equilibration protocol encompassing thiol reduction and alkylation was compared with a one‐step protocol employing continuous exposure to hydroxyethyl disulfide. Both equilibration protocols gave equally well‐resolved spot maps with analytical protein loads regardless of IPG strip pH range. Using preparative protein loads, narrow range IPG strips gave comparable results for the two protocols while preparative load on wide range IPG strips was the only condition where classical reduction/alkylation outperformed hydroxyethyl disulfide equilibration. Moreover, with analytical protein loads, the hydroxyethyl disulfide equilibration time could be significantly reduced without apparent loss of spot map quality or quantitative protein transfer from the first‐ to the second dimension gel. MALDI‐TOF mass spectrometric protein identification was successfully performed with either iodoacetamide or hydroxyethyl disulfide as the cysteine modifier, yielding comparable identification results with high confidence in protein assignment, sequence coverage, and detection of cysteine‐containing peptides. The results provide a novel and simplified protocol for 2‐DE where the concept of hydroxyethyl disulfide as the cysteinyl protecting agent is extended to cover the entire 2‐D work flow.
Proteomic analysis on the expression of outer membrane proteins of Vibrio alginolyticus at different sodium concentrations
Authors: Xu Changxin , Wang Sanying , Ren Haixia , Lin Xiangmin , Wu Lina , Peng Xuanxian
Published: July 2005

The ability of osmoregulation is crucial to marine pathogens that always face the change of osmotic pressure when they shift between natural marine water‐bodies and hosts. Previous studies indicated that the expressional patterns of outer membrane proteins (OMPs) changed when Gram‐negative bacteria were transferred in different environments. In the present study, proteomic methodologies were used to investigate the expressional pattern of OMPs of Vibrio alginolyticus, a universal marine pathogen, at different Na+ concentrations. OmpW, OmpV, and Omp TolC were determined to be osmotic stress responsive proteins. Of the three proteins, importantly, OmpV and OmpW showed distinctly reverse changes to each other, indicating that the two proteins might be the two components varied with changed NaCl concentrations. In addition, our results suggest that closely related species of bacteria with available whole genomic databases should be applied after item microorganism species was used when proteins from a bacterium with unavailable whole genomic information were identified by PMF. Therefore, our results not only expand our knowledge on osmotic stress responsive proteins, but also provide valuable information for strategies on screening of these proteins.
Report of the roundtable discussion organised by the Swiss Proteomics Society (SPS), Bern, 8th December 2004
Authors: Noukakis Dimitrios , Gadola Stephan , Stöcklin Reto
Published: July 2005

How close are we to using proteomics tools in the every day practice of physicians? What are the socio‐economical issues our health care system may face with the advent of biomarkers for early diagnosis? How to get the specialists from the various disciplines integrated in proteomics to establish a common understanding of the clinical issues and develop the necessary standards (methods, biochemicals and IT)? These were the kind of questions a panel of specialists tried to answer during the roundtable discussion that took place in Bern during the Swiss Proteomics Society 2004 congress.
Copolymerization with the feeding of one of the comonomers: Cationic activated monomer copolymerization of ε‐caprolactone with ethylene oxide
Authors: Bednarek Melania , Kubisa Przemysław
Published: July 2005

The cationic copolymerization of ε‐caprolactone with ethylene oxide (EO) under the conditions of activated monomer polymerization, that is, with a low‐molecular‐weight diol as an initiator and BF3 etherate as a catalyst, was studied. To ensure the uniform composition of the resulting copolymers (telechelic oligodiols), the copolymerization was conducted with incremental feeding of the EO comonomer, which was more reactive in the cationic process. 1H NMR analysis of samples isolated at different stages of the copolymerization indicated that the average composition of the copolymer was indeed nearly constant over the course of the copolymerization. Matrix‐assisted laser desorption/ionization time‐of‐flight spectra of the products revealed, however, that for the same degree of polymerization, macromolecules containing different numbers of EO units were present. The observed distribution was compared with the distribution simulated under the assumption that the probability of incorporating a given unit depended only on the feed composition (nearly constant during the copolymerization). With this assumption, a good agreement between the observed and simulated spectra was obtained. This indicated that, even when the optimum conditions for the formation of a uniform copolymer were created, the individual macromolecules differed in composition because of the statistical character of the copolymerization. The results of differential scanning calorimetry analysis were compatible with such a conclusion; two melting peaks appeared on differential scanning calorimetry curves when a sample was heated immediately after fast cooling, and this may indicate the presence of different types of crystallites. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3788–3796, 2005
Time‐resolved method for the measurement of volume changes during polymerization
Authors: Holst Marco , Schänzlin Katharina , Wenzel Mirko , Xu Jianjun , Lellinger Dirk , Alig Ingo
Published: July 2005

A new laser scanning dilatometer, based on a simplified capillary‐type dilatometer using a laser scan micrometer for the detection of changes of the sample dimension, is described. The method can be applied to time‐resolved measurements of volume changes for transparent and nontransparent samples. The time resolution of the setup is below 1 s, the absolute error in determining the volume change is below 0.0004 cm3, and the accuracy of the measured shrinkage is better than 0.2 vol. %. The operation temperature ranges from room temperature to 160 °C. The setup has been applied to the investigation of the volume shrinkage during the curing of epoxy resins [diglycidyl ether of bisphenol A (DGEBA)] without and with fillers. Furthermore, the effect of a phase transformation on the volume has been demonstrated by the melting of a crystalline phase (succinic anhydride) dispersed in a DGEBA matrix due to the heat of reaction. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2314–2325, 2005
Kinetically controlled phase transitions in liquid‐crystalline polymers. III. Influence of the molecular weight and annealing temperature on two‐dimensional K phase formation in a side‐chain polyacrylate
Authors: Boiko N. I. , Shibaev V. P. , Kozlovsky M.
Published: July 2005

Narrow fractions of a side‐chain acrylate oligomer/polymer with phenyl benzoate side chains are separated in a broad range of the degree of polymerization (7 ≤ Pw ≤ 149). An examination of the phase behavior of the obtained fractions has shown that only the longer macromolecules can form the two‐dimensional K (TDK) mesophase, whereas oligomers of a shorter main chain form the conventional nematic phase only. A critical Pw value has been observed to be necessary for the TDK mesophase formation. The temperatures and enthalpies of liquid‐crystalline phase transitions have been studied as a function of the molar mass, and the phase‐growth kinetics for the TDK phase have been studied with an Avrami treatment. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2352–2360, 2005
Crystallization of poly(butylene adipate) in the presence of nucleating agents
Authors: Kai Weihua , Zhu Bo , He Yong , Inoue Yoshio
Published: July 2005

The effect of nucleating agents on the polymorphic crystallization behavior of poly(butylene adipate) (PBA) was studied with four kinds of commercially available nucleating agents, such as talc and boron nitride. The crystal structures of the α and β forms were studied with wide‐angle X‐ray diffraction. The β‐to‐α‐crystal transformation of PBA in the absence and presence of the nucleating agents in isothermal crystallization and nonisothermal crystallization processes was studied with differential scanning calorimetry and polarized optical microscopy. In both isothermal and nonisothermal crystallization, the introduction of nucleating agents selectively initiated the nucleation of the α‐form crystal, which was relatively slow in the absence of nucleating agents. The nucleating activity of the four kinds of nucleating agents in the crystallization of the PBA α‐form crystal was determined by the study of the nonisothermal crystallization, spherulite morphology, and isothermal kinetics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2340–2351, 2005
Loop‐closure events during protein folding: Rationalizing the shape of Φ‐value distributions
Authors: Weikl Thomas R.
Published: July 2005

In the past years, the folding kinetics of many small single‐domain proteins has been characterized by mutational Φ‐value analysis. In this article, a simple, essentially parameter‐free model is introduced which derives folding routes from native structures by minimizing the entropic loop‐closure cost during folding. The model predicts characteristic folding sequences of structural elements such as helices and β‐strand pairings. Based on few simple rules, the kinetic impact of these structural elements is estimated from the routes and compared to average experimental Φ‐values for the helices and strands of 15 small, well‐characterized proteins. The comparison leads on average to a correlation coefficient of 0.62 for all proteins with polarized Φ‐value distributions, and 0.74 if distributions with negative average Φ‐values are excluded. The diffuse Φ‐value distributions of the remaining proteins are reproduced correctly. The model shows that Φ‐value distributions, averaged over secondary structural elements, can often be traced back to entropic loop‐closure events, but also indicates energetic preferences in the case of a few proteins governed by parallel folding processes. Proteins 2005. © 2005 Wiley‐Liss, Inc.
How well are protein structures annotated in secondary databases?
Authors: Rother Kristian , Michalsky Elke , Leser Ulf
Published: July 2005

We investigated to what extent Protein Data Bank (PDB) entries are annotated with second‐party information based on existing cross‐references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear “annotation gap” for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well‐annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The Gō model revisited: Native structure and the geometric coupling between local and long‐range contacts
Authors: Faísca Patrícia F. N. , Telo da Gama Margarida M. , Nunes Ana
Published: July 2005

Monte Carlo simulations show that long‐range interactions play a major role in determining the folding rates of 48‐mer three‐dimensional lattice polymers modeled by the Gō potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long‐range interactions to the native state's energy is decreased from ∼50% towards zero. However, the dispersion of the simulated folding times is strongly dependent on native geometry and Gō polymers folding to one of the target structures exhibits folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long‐range contacts, which means that, when this coupling exists, the formation of long‐range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling results in a kinetics that is more sensitive to the interaction energy parameters; in this case, the formation of local contacts is not capable of promoting the establishment of long‐range ones when the latter are strongly penalized energetically and this results in longer folding times. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The “first in–last out” hypothesis on protein folding revisited
Authors: Pintar Alessandro , Pongor Sándor
Published: July 2005

We calculated profiles for mean residue depth, contact order, and number of contacts in the native structure of a series of proteins for which folding has been studied extensively, the chymotrypsin inhibitor 2, the SH3 module from the src tyrosine kinase, the small ribonuclease barnase, the bacterial immunity protein Im7, and apomyoglobin. We compared these profiles with experimental data from equilibrium or pulse labeling hydrogen‐deuterium exchange obtained from NMR and ϕ values obtained from the protein engineering approach. We find a good qualitative agreement between the hierarchy of formation of topological elements during the folding process and the ranking of secondary structure elements in terms of residue depth. Residues that are most deeply buried in the core of the native protein usually belong to stretches of secondary structure elements that are formed early in the folding pathway. Residue depth can thus provide a useful and simple tool for the design of folding experiments. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily
Authors: Liger Dominique , Quevillon‐Cheruel Sophie , Sorel Isabelle , Bremang Michael , Blondeau Karine , Aboulfath Ilham , Janin Joël , van Tilbeurgh Herman , Leulliot Nicolas
Published: July 2005

In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 Å resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the “hot dog” fold, identifies the protein as a “kinked double hot dog” fold. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Fibre composite structures in Australia's civil engineering market: an anatomy of innovation
Authors: Van Erp Gerard , Cattell Craig , Heldt Tim
Published: July 2005

During the last 5–10 years there has been considerable activity in research and development of fibre composites in the Australian civil engineering market. Areas of activity have included; bridge systems, replacement of large‐section hardwood girders, waterfront structures and railway sleepers. The work has involved not only the initial concept development, but also the construction and deployment of full‐scale prototypes. Through close involvement of major asset owners, including state road and rail authorities and city councils, these technologies have evolved from initial technology demonstrators to become viable commercial alternatives to traditional structural solutions. This paper presents a review of these developments and examines the process involved in taking these new systems from a novelty to a viable and credible alternative for local asset owners.
Method for the analysis of nonselective spectra of optically stimulated electron emission from irradiated dielectrics
Authors: Zatsepin A. F. , Biryukov D. Yu. , Kortov V. S.
Published: July 2005

A method has been proposed and substantiated for processing of nonselective optically stimulated electron emission (OSEE) spectra of irradiated crystalline and amorphous dielectrics. This method allows the separation of the emission contribution of discrete centers taking into account effects of radiation‐induced electrization of materials and the unsteady state of the electron emission. Separation of OSEE selective bands facilitates the establishment of the origin of discrete emission‐active centers and makes it possible to estimate the concentration and parameters of radiation defects localized in surface layers. The quantum yields of OSEE and ionization barriers of optically excited defects are calculated using kinetic and corrected isochronal temperature dependences of the emission current. Some capabilities of the method have been demonstrated by an example of glassy SiO2 and crystalline Be2SiO4. Oxygen‐deficient centers (ODCs), bulk and surface E′‐centers, and also non‐bridging oxygen hole centers (NBOHCs) have been recorded. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth Parameters and Substrate Treatment for the MOCVD Growth of ZnO
Authors: Wang Jinzhong , Sallet Vincent , Amiri Gaëlle , Rommeluère Jean‐François , Lusson Alain , Rzepka E. , Lewis John E. , Galtier Pierre , Gorochov Ouri
Published: July 2005

ZnO films were grown on sapphire substrates using vertical MOCVD system with DEZn and tertiary‐butanol as precursors, respectively. The benefits of substrate treatment on the microstructure and morphology of the film were shown. The influences of growth temperature and partial pressure ratio RVI/II on crystal quality were investigated in detail. XRD, Electron Channeling Pattern and Raman spectra indicated that the highest crystal quality film was grown at 425 °C when the partial pressure ratio of tertiary‐butanol (t‐Bu) to diethylzinc (DEZn) was 8. X‐ray rocking curves exhibit Full Width at Half Maximum (FWHM) of 607 arcsec. A strong exciton emission peak appears in the photoluminescence (PL) spectra. Furthermore, the peak position has a slight shift to low energy with increase of the growth temperature. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Vertical chip of GaN‐based light‐emitting diode formed on sapphire substrate
Authors: Kim Seong‐Jin , Choi Yong‐Seok , Han Young‐Heon , Kim Chang‐Yeon , Yu Soon‐Jae , Kim Song‐Gang
Published: July 2005

In order to improve GaN‐based light‐emitting diode (LED) performance, a sapphire‐etched vertical‐electrode nitride semiconductor (SEVENS) LED is fabricated by a chemical wet etching technique. The light‐output power, heat dissipation, and reverse electrostatic discharge (ESD) characteristics of SEVENS‐LED are improved compared to those of the conventional NiAu lateral‐electrode (LE) GaN‐based LED formed on the sapphire substrate. The 20 mA light‐output power and reverse ESD pulse amplitude of SEVENS‐LED are approximately 4.5 mW and 2000 V, respectively. The improved LED performance is attributed to changing a lateral electrode to a vertical electrode although the sapphire substrate is not transferred to a conducting substrate. The device fabrication method will be useful for providing us high‐brightness and high‐power GaN‐based LEDs for future solid‐state general lighting applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural and electro‐optical characteristics of Ga‐doped ZnO films prepared by thermal oxidation of metallic Zn100–xGax films
Authors: Mohamed S. H.
Published: July 2005

Ga‐doped ZnO thin films have been obtained by thermal oxidation of electron beam evaporated metallic Zn100–xGax thin films. The structural, optical, and electrical resistivity of the oxidized films depend on Ga content. The value of oxidation temperature shifts to higher temperatures with increasing Ga content. After oxidation, polycrystalline ZnO phase is formed and no Ga2O3 peaks are found. The Ga content is found to affect transmittance strongly and the optical bandgap slightly. The optical bandgap values of the oxidized Ga‐doped films are comparable at higher oxidation temperatures. Depending on the Ga content, the electrical resistivity increases with increasing oxidation temperature. At 550 °C all the Ga‐doped films have electrical resistivity values around 105 Ω cm. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Density functional theory study of the relative energies and structures of the chair, twist, and boat conformations of stannacyclohexane, 1‐methylstannacyclohexane, and 1,1‐dimethylstannacyclohexane
Authors: Freeman Fillmore , Fang Christine , Hoang David V. , Trinh Khue M.
Published: July 2005

The relative energies and structures of the chair, twist, and boat conformations of stannacyclohexane, 1‐methylstannacyclohexane, and 1,1‐dimethylstannacyclohexane have been investigated using density functional theory (DFT) (BLYP, B3LYP, B3P86, B3PW91) and hybrid Hartree–Fock/DFT (BH and HLYP) methods with the SDD basis set. The five levels of theory predicted similar energy differences (Erel) among the respective conformations of the stannacyclohexanes. Similar equilibrium geometries were also predicted at the five theoretical levels, with BLYP giving the longest bonds and BH and HLYP giving the shortest bonds. B3LYP predicted the chair conformer of stannacyclohexane to be 3.09, 3.47, and 4.27 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The chair conformer of axial 1‐methylstannacyclohexane is 2.85, 3.40, and 4.46 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state and the chair conformer of equatorial 1‐methylstannacyclohexane is 3.05, 3.52, and 4.56 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The chair conformer of axial 1‐methylstannacyclohexane is 0.19 kcal/mol less stable than the equatorial chair conformer, and the chair conformer of 1,1‐dimethylstannacyclohexane is 2.94, 3.49, and 4.21 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The relative energies (Erel) of the conformers of the stannacyclohexanes are also compared with the available experimental and theoretical relative energies of the corresponding cyclohexanes and silacyclohexanes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Quantum study of the structure of the active site of methylamine dehydrogenase
Authors: Pierdominici‐Sottile Gustavo , Echave Julián , Palma Juliana
Published: July 2005

In this article we present the results of a quantum study performed on different models of the active site of methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. During the rate‐determinant step of the reaction, a proton is transferred from the methyl group of the substrate to one of the bases of the active site. We performed calculations on three different models of the active site. The number of atoms of the models ranges from 68 to 95. Minimizations and optimizations were performed at the PM3 level of theory. The energies of the optimized structures were then recalculated at the B3LYP 6‐31G(d) level. From these energies, we calculated the barriers for H+ transfer toward the putative acceptors of the proton Asp76 and Thr122. By comparing the results of different models against each other, we drew some conclusions about the role of different residues. We found that the H+ transfer from the substrate toward Thr122 requires that this residue be ionized. The estimated barrier for this ionization was found to be >19 kcal/mol. The barrier for H+ transfer from the substrate toward Asp76 is significantly smaller. Our best estimates indicate that this barrier is 9.7 kcal/mol, when the imino group of the substrate is unprotonated and 7.7 kcal/mol when it is protonated. We thoroughly discussed the agreement and disagreement of these values with the results reported in previous theoretical and experimental studies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005