bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of a thioredoxin‐related protein‐1 is induced by prostaglandin E2
Authors: Kim Kye Young , Lee June Woo , Park Min Seon , Jung Myeong Ho , Jeon Gyoung A , Nam Myeong Jin
Published: October 2005

Prostaglandin E2 (PGE2) plays an important role in protection of the gastric mucosa against various damaging agents and growth‐inhibitory activity on tumor cells. However, the precise regulation mechanism of PGE2 in gastric cancer cells is still unclear. In this study, we isolated a gene, which is regulated by PGE2 in SNU‐1, human gastric adenocarcinoma cells, using differential display RT‐PCR (DD RT‐PCR) and characterized the function of the gene induced by PGE2. The full‐length cDNA of the gene was cloned by the rapid amplification of cDNA ends method. The 1659 base pair cDNA consists of a 30‐nt 5′‐noncoding region, an 891‐nt open reading frame and a 738‐nt 3′noncoding region that includes a poly (A) signal. As a result of protein motif search, we found that it has a conserved thioredoxin‐active site, Cys‐Gly‐Pro‐Cys and a Myb‐DNA binding domain repeat signature. Thus, we designated this gene product as thioredoxin‐related protein‐1, TRP‐1. TRP‐1 was expressed in a lower extent in renal, gastric and colon cancer tissues and is translated into 33 kDa protein in nuclear and cytoplasmic fractions. TRP‐1 has a thioredoxin activity, which was detected using the insulin disulfide reduction assay. Another potential role of TRP‐1 is repression of B‐Myb activity through direct binding to B‐Myb, a transcriptional factor induced at G1–S transition. Finally, TRP‐1 overexpression inhibits mammalian cell proliferation and specifically predispose to G0/G1 phase arrest. In conclusion, these results imply that TRP‐1 is a mammalian thioredoxin and plays as a transcriptional repressor through direct binding to the transcription factor B‐Myb. © 2005 Wiley‐Liss, Inc.
Long‐Chain Branching and Rheological Properties of Ethylene‐1‐Hexene Copolymers Synthesized from Ethylene Stock by Concurrent Tandem Catalysis
Authors: Ye Zhibin , AlObaidi Fahad , Zhu Shiping , Subramanian Ramesh
Published: October 2005

Summary: Concurrent tandem catalysis systems have shown a significant advantage in the convenient synthesis of linear low‐density polyethylene (LLDPE) from a sole ethylene monomer stock by uniquely coupling the tandem action between an ethylene oligomerization catalyst and an ethylene copolymerization catalyst in a single reactor. Recently, we have reported the successful synthesis of ethylene‐hexene derived LLDPE using an effective concurrent tandem catalysis system comprising (η5‐C5H4CMe2C6H5)TiCl3 (1)/MMAO and a CGC copolymerization catalyst, [(η5‐C5Me4)SiMe2(tBuN)]TiCl2 (2)/MMAO. In this work, we report the results from an extensive study on the important rheological properties of LLDPE grades prepared with this tandem catalysis system. Two sets of LLDPE samples having different short‐chain branching density (SCBD) were prepared with the tandem catalysis system under various catalyst concentrations and at temperatures of 25 and 45 °C. The melt rheological properties of these polymers were evaluated using small‐amplitude dynamic oscillation measurements. These polymers have been found to possess typical rheological properties found in long‐chain branched (LCB) polymers, such as enhanced zero‐shear viscosity (η0), improved shear‐thinning, elevated dynamic moduli, and thermorheological complexity, which indicate the presence of long‐chain branching in the polymers. The long‐chain branching density (LCBD) of the two respective sets of polymers were qualitatively compared and correlated to the polymerization conditions including catalyst ratio and temperature. This work represents the first study on the rheological properties of LLDPE synthesized with concurrent tandem catalysis, and it discloses another appealing feature of this unique approach—its ability to produce LCB LLDPE from a single ethylene monomer stock.

Synthesis of linear low‐density polyethylene (LLDPE) from ethylene using ethylene oligomerization catalyst and an ethylene copolymerization catalyst.

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Synthesis of linear low‐density polyethylene (LLDPE) from ethylene using ethylene oligomerization catalyst and an ethylene copolymerization catalyst.
Neutral Polymeric Surfactants Derived from Dextran: A Study of Their Aqueous Solution Behavior
Authors: Rotureau Elise , Chassenieux Christophe , Dellacherie Edith , Durand Alain
Published: October 2005

Summary: Amphiphilic polysaccharides are obtained by hydrophobic modification of a neutral bacterial polysaccharide, dextran. By reacting the polysaccharide with aliphatic epoxides (epoxyoctane and epoxydodecane) in dimethyl sulfoxide, a series of amphiphilic polymers is obtained which covers a large range of structural parameters (length of the polysaccharide, number and nature of hydrocarbon moieties). The solution behavior of dextran derivatives is first characterized by viscometric measurements in dilute and semi‐dilute domains. The effects of molecular parameters on polymer viscosity behavior are evidenced and discussed. Information on the state of aggregation of polymers is obtained by the use of static and dynamic light scattering. The presence of aggregates in the dilute domain is clearly evidenced and their structural characteristics are estimated (size, molecular weight and number of aggregation). The aggregates are shown to account for the viscometric results in the examined concentration range, relating their chemical parameters (hydrodynamic radius and molecular weight) to the macroscopic behavior of the solutions.

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Study of the Fragmentation Process of Different Supports for Metallocenes by Laser Scanning Confocal Fluorescence Microscopy (LSCFM)
Authors: Jang Yong‐Jun , Naundorf Corinna , Klapper Markus , Müllen Klaus
Published: October 2005

Summary:The fragmentation of supports, a key issue for the polymerization of olefins via supported metallocene catalysts, was investigated by laser scanning confocal fluorescence microscopy (LSCFM). Metallocenes were immobilized on silica and on two organic supports, namely polystyrene latex particles and a polystyrene resin, which were stained by fluorescent perylene dyes. All supported catalysts showed different activities in the ethylene polymerization under the same reaction conditions. Recording fluorescence images of the polyolefin product beads at different polymerization times by LCSFM proved different fragmentation processes for the catalyst. While for the µm‐sized polystyrene resins almost no fragmentation was observed, supports based on aggregated latex particles fragmented throughout the bead from the beginning, corresponding to the multi‐grain model established for Ziegler‐catalysts. For the silica particles a fragmentation starting from the outer spheres to the core was detected, confirming in a fast and easy way the layer‐by‐layer model developed by electron microscopy studies.

SEM images of the catalyst supported on (A) microsized PS beads, (B) nanosized PS beads and (C) silica gel.

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SEM images of the catalyst supported on (A) microsized PS beads, (B) nanosized PS beads and (C) silica gel.
Core Functionality and Scaling Behavior of Lysine Dendrimers
Authors: Fritzinger Bernd , Appelhans Dietmar , Voit Brigitte , Scheler Ulrich
Published: October 2005

Summary: A scaling exponent to describe the dependence of the hydrodynamic radius as a characteristic length of the molecule on the molecular weight, has been determined for low generation dendrimers with a thiacalixarene core and lysine dendrons. The hydrodynamic radius has been calculated from the diffusion coefficient measured by pulsed‐field‐gradient NMR spectroscopy. Scaling exponents of 2.0 for the lysine monodendron, 2.3 for a dendrimer with a bifunctional core, and 3.9 for a dendrimer with a tetrafunctional core have been determined. For a given structure of the dendrons, the scaling exponent reflects the functionality of the core of the dendrimers.

Hydrodynamic radius of lysine dendrons as a function of molar mass.

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Hydrodynamic radius of lysine dendrons as a function of molar mass.
Fabrication of Electrically Conducting Polypyrrole‐Poly(ethylene oxide) Composite Nanofibers
Authors: Nair Sujith , Natarajan Sudarshan , Kim Seong H.
Published: October 2005

Summary: Electrically conducting polypyrrole‐poly(ethylene oxide) (PPy‐PEO) composite nanofibers are fabricated via a two‐step process. First, FeCl3‐containing PEO nanofibers are produced by electrospinning. Second, the PEO‐FeCl3 electrospun fibers are exposed to pyrrole vapor for the synthesis of polypyrrole. The vapor phase polymerization occurs through the diffusion of pyrrole monomer into the nanofibers. The collected non‐woven fiber mat is composed of 96 ± 30 nm diameter PPy‐PEO nanofibers. FT‐IR, XPS, and conductivity measurements confirm polypyrrole synthesis in the nanofiber.

An SEM image of the PPy‐PEO composite nanofibers. The scale bar in the image is 500 nm.

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An SEM image of the PPy‐PEO composite nanofibers. The scale bar in the image is 500 nm.
A New Poly(fluorene‐co‐carbazole) with a Large Substituent Group at the 9‐Position of the Carbazole Moiety: An Efficient Blue Emitter
Authors: Du Junping , Fang Qiang , Bu Dongsheng , Ren Shijie , Cao Amin , Chen Xiaoyao
Published: October 2005

Summary: A new poly(fluorene‐co‐carbazole) (PFC‐1) with a large substituent group (ADN, a naphthalene‐anthracene derivative moiety) at the 9‐position of carbazole was synthesized. Compared with poly(fluorene‐co‐carbazole)s that have an alkyl substituent group at the 9‐position of the carbazole, the UV‐vis absorption (or photoluminescent emission) peaks of PFC‐1 are in almost the same position both in solution and in the solid state, whereas films of the former give peaks at longer wavelengths than those in solution. The photoluminescent (PL) spectra of PFC‐1 indicate that the attachment of ADN to the poly(fluorene‐co‐carbazole)s gives rise to an efficient blue emission from non‐aggregated ADN. There is no difference evident between PFC‐1 and other reported poly(fluorene‐co‐carbazole)s in PL quantum yield, thermostability, and electrochemical behavior, which suggests that PFC‐1 is an efficient blue emitter.

UV‐Vis spectra of the poly(fluorene‐co‐carbazole) (PFC‐1), with a large substituent group (ADN, a naphthalene‐anthracene derivative moiety) at the 9‐position of carbazole, in toluene and in the film.

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UV‐Vis spectra of the poly(fluorene‐co‐carbazole) (PFC‐1), with a large substituent group (ADN, a naphthalene‐anthracene derivative moiety) at the 9‐position of carbazole, in toluene and in the film.
Novel Amphiphilic Diblock and Triblock Liquid‐Crystalline Copolymers with Well‐Defined Structures Prepared by Atom Transfer Radical Polymerization
Authors: Yu Haifeng , Shishido Atsushi , Ikeda Tomiki , Iyoda Tomokazu
Published: October 2005

Summary: Based on a hydrophilic poly(ethylene oxide) macroinitiator (PEOBr), a novel amphiphilic diblock copolymer PEO‐block‐poly(11‐(4‐cyanobiphenyloxy)undecyl) methacrylate) (PEO‐b‐PMA(11CB)) was prepared by atom transfer radical polymerization (ATRP) using CuCl/1,1,4,7,10,10‐hexamethyltriethylenetriamine as a catalyst system. An azobenzene block of poly(11‐[4‐(4‐butylphenylazo)phenoxyl]undecyl methacrylate) was then introduced into the copolymer sequence by a second ATRP to synthesize the corresponding triblock copolymer PEO‐b‐PMA(11CB)‐b‐PMA(11Az). Both of the amphiphilic block copolymers had well‐defined structures and narrow molecular‐weight distributions, and exhibited a smectic liquid‐crystalline phase over a wide temperature range.

The amphiphilic triblock copolymer synthesized here.

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The amphiphilic triblock copolymer synthesized here.
Back Cover: Macromol. Rapid Commun. 20/2005
Authors: Nair Sujith , Natarajan Sudarshan , Kim Seong H.
Published: October 2005

Back Cover: PPy‐PEO composite nanofibers with an average size 96 ± 30 nm are synthesized by vapor phase polymerization of pyrrole over electrospun PEO‐FeCl3 fibers. The pyrrole monomer vapor diffuses into the nanofibers and is oxidatively polymerized by FeCl3 into polypyrrole. Further details can be found in the Communication by S. Nair, S. Natarajan, and S. H. Kim* on page 1599.
Entropic Sampling of Free and Ring Polymer Chains
Authors: Volkov Nikolai A. , Yurchenko Anton A. , Lyubartsev Alexander P. , Vorontsov‐Velyaminov Pavel N.
Published: October 2005

Summary: We extend Monte Carlo (MC) methods developed in our previous paper (J. Phys. A, Math. Gen. 2004, 37, 1573) and based on entropic sampling within Wang‐Landau (WL) algorithm to the simulation of lattice and continuous models of ring polymers. For a continuous freely joined ring chain (an equilateral polygon) with hard sphere monomer units, the excess entropy of rings relative to the corresponding reference system, a phantom ring chain, is obtained. The excess specific entropy is calculated for a set of various diameters of monomer units d and chain lengths N. Its limiting values for $N\to \infty$ ($N^{-1}\to 0$) are estimated for each d and coincidence with those for corresponding free chains is demonstrated. We also develop a WL approach to calculate thermal properties of free and ring continuous chains with an Lennard‐Jones attraction between nonbonded beads being added to hard core repulsion at fixed d. The obtained energy distributions provide calculation of canonical properties such as conformational energy, heat capacity, entropy, and mean square radius of inertia. Thermal results for free and ring chains are being finally compared. Analogous calculations are performed for lattice‐free chains and rings.

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Weighted Poincaré and Korn inequalities for Hölder α domains
Authors: Acosta Gabriel , Durán Ricardo G. , Lombardi Ariel L.
Published: October 2005

It is known that the classic Korn inequality is not valid for Hölder α domains. In this paper, we prove a family of weaker inequalities for this kind of domains, replacing the standard Lp‐norms by weighted norms where the weights are powers of the distance to the boundary.

In order to obtain these results we prove first some weighted Poincaré inequalities and then, generalizing an argument of Kondratiev and Oleinik, we show that weighted Korn inequalities can be derived from them.

The Poincaré type inequalities proved here improve previously known results.

We show by means of examples that our results are optimal. Copyright © 2005 John Wiley & Sons, Ltd.
Visualization of material stiffness in geomechanics analysis
Authors: Wotring Donald C. , Hashash Youssef M. A.
Published: October 2005

This paper presents novel visualization techniques to simplify representation of the fourth‐order material stiffness tensor as a set of three‐dimensional geometric objects. Stiffness visualization aids in understanding the complex stiffness characteristics of highly non‐linear constitutive models including modelled material anisotropy and loading path dependent stiffness variation. Stiffness visualization is relevant for understanding the relationship of material stiffness to global behaviour in the analysis of a boundary value problem. The spherical pulse stiffness visualization method, developed in the acoustics field, is extended to visualize stiffness of geomaterials using three three‐dimensional objects. This method is limited to relatively simple constitutive models with symmetric stiffness matrices insensitive to loading magnitude and direction. A strain dependent stiffness visualization method is developed that allows the examination of material stiffness for a range of loading directions and is suitable for highly non‐linear and path dependent material models. The proposed stiffness visualization can be represented as 3‐D, 2‐D and 1‐D objects. The visualization technique is used to represent material stiffness and its evolution during simulated soil laboratory tests and deep excavation construction. Copyright © 2005 John Wiley & Sons, Ltd.
Catalytic dehydrogenation of ethane over mononuclear Cr(III)–silica surface sites. Part 2: CH activation by oxidative addition
Authors: Lillehaug Sindre , Jensen Vidar R. , Børve Knut J.
Published: October 2005

Models of Cr(III)–silica were used to study CH activation in ethane by oxidative addition as a possible route to catalytic dehydrogenation. This mechanism involves a formal double oxidation of chromium and a minimum energy crossing point (MECP) was located on the seam between the quartet spin potential energy surface of Cr(III) and the doublet spin potential energy surface of Cr(V). Subsequent to the change of spin state, the CH activation path passes through a transition state on the doublet potential surface, leading to the formation of an ethylhydridochromium(V) complex. This complex represents only a shallow minimum on the potential energy surface and β‐hydrogen transfer to complete the catalytic cycle must therefore take place in the extension of the CH activation step. The combination of a significant activation energy and a small pre‐exponential factor in the rate constant makes CH activation by oxidative addition an unlikely mechanism for dehydrogenation in this system. Copyright © 2005 John Wiley & Sons, Ltd.
Star‐shaped poly(L‐lactide)s with variable numbers of hydroxyl groups at polyester arms chain‐ends and directly attached to the star‐shaped core—Controlled synthesis and characterization
Authors: Biela Tadeusz , Duda Andrzej , Pasch Harald , Rode Karsten
Published: October 2005

Star‐shaped poly(L‐lactide)s (PLAs) bearing variable numbers of secondary hydroxyl groups at linear arms chain‐ends and primary hydroxyl groups directly attached to dipentaerithritol core (DPE) ((HO)6−xDPE(PLA‐OH)x, where x = 1–6) were prepared and then analyzed by means of size exclusion chromatography (SEC), 1H NMR spectroscopy, MALDI‐TOF mass spectrometry, and eventually by Liquid Chromatography at Critical Conditions (LC‐CC). First, starting from DPE(OH)6 a series of polyols with various number of hydroxyl groups has been obtained ((BnO)6−xDPE(OH)x, where Bn denotes benzyl moiety and x = 1–6). The living ring‐opening polymerization of L‐lactide (LA) with (BnO)6−xDPE(OH)x/tin(II) octoate mixtures as initiating and catalytic system led to star‐shaped (BnO)6−xDPE(PLA‐OH)x polymers with molar masses (Mn) controlled by LA and DPE concentrations ratio in the feed. Finally, deprotection (via hydrogenation) gave a series of (HO)6−xDPE(PLA‐OH)x PLA's. SEC (with Multiangle Laser Light Scattering Detector (MALLS)), NMR, and MALDI‐TOF analyses confirmed the assumed structures and Mn's of the prepared (BnO)6−xDPE(PLA‐OH)x and (HO)6−xDPE(PLA‐OH)x PLA's. LC‐CC measurements revealed that for (BnO)6−xDPE (PLA‐OH)x series the elution volumes increase monotonically with the increasing number of –PLA‐OH arms in one macromolecule and are independent on the given PLA molar mass because of the critical conditions. Contrary to the polymers having the protected core hydroxyl groups, the elution volume for (HO)6−xDPE(PLA‐OH)x series decreases with the increasing number of ‐PLA‐OH arms reaching a minimum value for 4‐arm PLA and then slightly increases for 5‐ and 6‐arm PLA. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6116–6133, 2005
Studies on the modification of poly(ω‐bromoalkyl‐1‐glycidylether)s with 4′‐methoxybiphenyl‐4‐oxy mesogenic groups
Authors: Montornés J. M. , Reina J. A. , Ronda J. C.
Published: October 2005

A series of poly[ω‐(4′‐methoxy‐biphenyl‐4‐oxy)alkyl‐1‐glycidylether]s were synthesized by chemically modifying the corresponding poly(ω‐bromoalkyl‐1‐glycidylether)s with the sodium salt of 4‐hydroxy‐4′‐methoxybiphenyl. New high‐molecular‐weight side‐chain liquid‐crystalline polymers were obtained with excellent yields and almost quantitative degrees of modification. They were all insoluble in THF and other common solvents. Characterization by 13C NMR confirmed that all the polymers had the expected structure. The liquid crystalline behavior of the polymers was analyzed by DSC and polarized optical microscopy, and mesophase assignments were confirmed by X‐ray diffraction studies. Polymers that had alkyl spacers with n = 2 and 4 were smectic C, those that had spacers with n = 6 and 8 were nematic cybotactic, and those that had longer spacers (n = 10 and 12) were smectic C again. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5998–6006, 2005
Synthesis and crosslinking reaction of poly(hydroxyurethane) bearing a secondary amine structure in the main chain
Authors: Ochiai Bungo , Nakayama Jun‐ichi , Mashiko Masayuki , Kaneko Yoshiro , Nagasawa Tomomi , Endo Takeshi
Published: October 2005

This article describes the polyaddition of bifunctional five‐membered cyclic carbonates and diethylenetriamine. The polyaddition proceeded via the selective addition of the primary amino group to the cyclic carbonates to give poly(hydroxyurethane)s bearing a secondary amine structure in the main chain. The resulting poly (hydroxyurethane) having a secondary amine structure was crosslinked by a reaction with a bifunctional dithiocarbonate to give a networked poly(hydroxyurethane–mercaptothiourethane). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5899–5905, 2005
Highly active copolymerization of ethylene with 10‐undecen‐1‐ol using phenoxy‐based zirconium/methylaluminoxane catalysts
Authors: Zhang Xiaofan , Chen Shangtao , Li Huayi , Zhang Zhicheng , Lu Yingying , Wu Chunhong , Hu Youliang
Published: October 2005

Activated with methylaluminoxane (MAO), phenoxy‐based zirconium complexes bis[(3‐tBu‐C6H3‐2‐O)‐CHNC6H5]ZrCl2, bis[(3,5‐di‐tBu‐C6H2‐2‐O)‐PhCNC6H5] ZrCl2, and bis[(3,5‐di‐tBu‐C6H2‐2‐O)‐PhCN(2‐F‐C6H4)]ZrCl2 for the first time have been used for the copolymerization of ethylene with 10‐undecen‐1‐ol. In comparison with the conventional metallocene, the phenoxy‐based zirconium complexes exhibit much higher catalytic activities [>107 g of polymer (mol of catalyst)−1 h−1]. The incorporation of 10‐undecen‐1‐ol into the copolymers and the properties of the copolymers are strongly affected by the catalyst structure. Among the three catalysts, complex c is the most favorable for preparing higher molecular weight functionalized polyethylene containing a higher content of hydroxyl groups. Studies on the polymerization conditions indicate that the incorporated commoner content in the copolymers mainly depends on the comonomer concentration in the feed. The catalytic activity is slightly affected by the Al(MAO)/Zr molar ratio but decreases greatly with an increase in the polymerization temperature. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5944–5952, 2005
Synthesis and characterization of carbon nanotube/polypyrrole core–shell nanocomposites via in situ inverse microemulsion
Authors: Yu Yijun , Ouyang Chu , Gao Yun , Si Zhihuai , Chen Wei , Wang Zhaoqun , Xue Gi
Published: October 2005

We demonstrate here a feasible approach to the preparation of multiwalled carbon nanotube (MWNT)/polypyrrole (PPy) core–shell nanowires by in situ inverse microemulsion. Transmission electron microscopy and scanning electron microscopy showed that the carbon nanotubes were uniformly coated with a PPy layer with a thickness of several to several tens of nanometers, depending on the MWNT content. Fourier transform infrared spectra suggested that there was strong interaction between the π‐bonded surface of the carbon nanotubes and the conjugated structure of the PPy shell layer. The thermal stability and electrical conductivity of the MWNT/PPy composites were examined with thermogravimetric analysis and a conventional four‐probe method. In comparison with pure PPy, the decomposition temperature of the MWNT/PPy (1 wt % MWNT) composites increased from 305 to 335 °C, and the electrical conductivity of the MWNT/PPy (1 wt % MWNT) composites increased by 1 order of magnitude. The current–voltage curves of the MWNT/PPy nanocomposites followed Ohm's law, reflecting the metallic character of the MWNT/PPy nanocomposites. The cyclic voltammetry measurements revealed that PPy/MWNT composites showed an enhancement in the specific charge capacity with respect to that of pure PPy. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6105–6115, 2005
External cross‐validation for unbiased evaluation of protein family detectors: Application to allergens
Authors: Soeria‐Atmadja Daniel , Wallman Mikael , Björklund Åsa K. , Isaksson Anders , Hammerling Ulf , Gustafsson Mats G.
Published: October 2005

Key issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10‐fold cross‐validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held‐out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Very fast empirical prediction and rationalization of protein pKa values
Authors: Li Hui , Robertson Andrew D. , Jensen Jan H.
Published: October 2005

A very fast empirical method is presented for structure‐based protein pKa prediction and rationalization. The desolvation effects and intra‐protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root‐mean‐square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Comparative molecular dynamics—Similar folds and similar motions?
Authors: Pang Andrew , Arinaminpathy Yalini , Sansom Mark S. P. , Biggin Philip C.
Published: October 2005

Proteins possessing the same fold may undergo similar motions, particularly if these motions involve large conformational transitions. The increasing amounts of structural data provide a useful starting point with which to test this hypothesis. We have performed a total of 0.29 μs of molecular dynamics across a series of proteins within the same fold family (periplasmic binding proteinlike) in order to address to what extent similarity of motion exists. Analysis of the local conformational space on these timescales (10–20 ns) revealed that the behavior of the proteins could be readily distinguished between an apo‐state and a ligand‐bound state. Moreover, analysis of the root‐mean‐square fluctuations reveals that the presence of the ligand exerts a stabilizing effect on the protein, with similar motions occurring, but with reduced magnitude. Furthermore, the conformational space in the presence of the ligand appears to be dictated by sequence but not by the type of ligand present. In contrast, apo‐simulations showed considerable overlap of conformational space across the fold as a result of their ability to undergo larger fluctuations. Indeed, we observed several transitions from different simulations between states corresponding to the closed‐cleft and open‐cleft forms of the fold, with the predominant motions being conserved across the different proteins. Thus, large‐scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Folding behavior of chaperonin‐mediated substrate protein
Authors: Xu Wei‐Xin , Wang Jun , Wang Wei
Published: October 2005

Chaperonin‐mediated protein folding is complex. There have been diverse results on folding behavior, and the chaperonin molecules have been investigated as enhancing or retarding the folding rate. To understand the diversity of chaperonin‐mediated protein folding, we report a study based on simulations using a simplified Gō‐type model. By considering effects of affinity between the substrate protein and the chaperonin wall and spatial confinement of the chaperonin cavity, we study the thermodynamics and kinetics of folding of an unfrustrated substrate protein encapsulated in a chaperonin cavity. The affinity makes the hydrophobic residues of the protein bind to the chaperonin wall, and a strong (or weak) affinity results in a large (or small) effect of binding. Compared with the folding in bulk, the folding in chaperonin cavity with different strengths of affinity shows two kinds of behaviors: one with less dependence on the affinity but more reliance on the spatial confinement effect and the other relying strongly on the affinity. It is found that the enhancement or retardation of the folding rate depends on the competition between the spatial confinement and the affinity due to the chaperonin cavity, and a strong affinity produces a slow folding while a weak affinity induces a fast folding. The crossover between two kinds of folding behaviors happens in the case that the favorable effect of confinement is balanced by the unfavorable effect of the affinity, and a critical affinity strength is roughly defined. By analyzing the contacts formed between the residues of the protein and the chaperonin wall and between the residues of the protein themselves, the role of the affinity in the folding processes is studied. The binding of the residues with the chaperonin wall reduces the formation of both native contacts and nonnative contact or mis‐contacts, providing a loose structure for further folding after allosteric change of the chaperonin cavity. In addition, 15 single‐site‐mutated mutants are simulated in order to test the validity of our model and to investigate the importance of affinity. Inspiringly, our results of the folding rates have a good correlation with those obtained from experiments. The folding rates are inversely correlated with the strength of the binding interactions, i.e., the weaker the binding, the faster the folding. We also find that the inner hydrophobic residues have larger effects on the folding kinetics than those of the exterior hydrophobic residues. We suggest that, besides the confinement effect, the affinity acts as another important factor to affect the folding of the substrate proteins in chaperonin systems, providing an understanding of the folding mechanism of the molecular chaperonin systems. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm
Authors: Tuffery Pierre , Derreumaux Philippe
Published: October 2005

Discretization of protein conformational space and fragment assembly methods simplify the search of native structures. These methods, mostly of Monte Carlo and genetic‐type, do not exploit, however, the fact that short fragments describing consecutive parts of proteins are conformation‐dependent. Yet, this information should be useful in improving ab initio and comparative protein structure modeling. In a preliminary study, we have assessed the possibility of using greedy algorithms for protein structure reconstruction based on the assembly of fragments of four‐residue length. Greedy algorithms differ from Monte Carlo and genetic approaches in that they grow a polypeptide chain one fragment after another. Here, we move one step further in complexity, and provide strong evidence that the dependence between consecutive local conformations during assembly makes possible the reconstruction of protein structures from their secondary structures using a Go potential. Overall our procedure can reproduce 20 protein structures of 50–164 amino acids within 2.7 to 6.5 Å RMSd and is able to identify native topologies for all proteins, although some targets are stabilized by very long‐range interactions. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Weighing in on a timeless controversy
Authors: Perry Jason
Published: October 2005

Timeless (Tim) and Period (Per) are coordinately synthesized interacting proteins that in response to positional/environmental cues comigrate to the nucleus as obligate heterodimers where they act to suppress their own gene expression as part of the circadian rhythm network in Drosophila. There has been considerable controversy about the structural nature of Tim because of somewhat conflicting results generated by the automated threading algorithm 3D‐PSSM. With use of a computer‐assisted but largely manual approach, it is shown here that Tim is composed of repetitive structural elements and that those elements comprise two ARM repeat domains, validating the essence of the original 3D‐PSSM prediction. Eleven individual ARM structural units are assigned, and a phylogenetic analysis showing their relatedness to one another is performed. In addition, there appears to be a small domain of prenyltransferase‐like repeats C‐terminal to the second ARM domain, which went undetected in previous analyses. Although we cannot know the precise conformation it adopts until a structure is solved, Tim emerges here as clearly a member of the helical repeat protein superfamily. Given its role in periodic nuclear translocation, Tim may, therefore, have a functional analogy with the photoperiod‐responsive protein Phor1 and other karyopherin‐like molecules. Proteins 2005. © 2005 Wiley‐Liss, Inc.
X‐ray topography of GdCa4O(BO3)3 single crystals grown by the Czochralski method
Authors: Wierzbicka E. , Kłos A. , Lefeld‐Sosnowska M. , Pajączkowska A.
Published: October 2005

GdCa4O(BO3)3 single crystals grown by the Czochralski technique were investigated by conventional transmission and back‐reflection X‐ray topography. The results were correlated with the growth conditions and stoichiometry of the crystals. Extended defects, especially dislocations, with different density, in samples cut perpendicular and parallel to the b‐axis were investigated. Long, straight dislocations lying perpendicular to [100] and [010] directions were observed. Periodical, small fluctuations of the diameter induced some defects. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large dielectric constant arising from space‐charge polarization in a SrTiO3 thin film grown on an YBa2Cu3O7–δ layer
Authors: Prijamboedi B. , Takashima H. , Wang R. , Shoji A. , Itoh M.
Published: October 2005

The frequency and temperature dependence of the dielectric constant of SrTiO3 (STO) thin‐film capacitors in multilayer structures of YBa2Cu3O7–δ/SrTiO3/YBa2Cu3O7–δ films were measured over the frequency range 100 to 106 Hz at 2–300 K. In a 750‐nm‐thick STO film, a low‐frequency dielectric dispersion gradually occurs in the temperature region below 50 K; at 5 K, the dielectric constant εr increases to 1.1 × 105 at frequencies below 103 Hz. A space‐charge polarization mechanism is responsible for the large observed dielectric constant of the STO thin films at low temperatures. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology of LiBr/LiF system studied by C‐AFM
Authors: Mazur P. , Gołek F.
Published: October 2005

In this work we investigate the growth of LiBr on LiF(100) by means of atomic force microscopy using its contact mode. To avoid electron or photon stimulated decomposition of the sample the substrate and the adlayer orientations were determined without use of any ionizing radiation. It is shown that LiBr deposited on the LiF(100) single crystal surface forms flat and well oriented layers. Furthermore, the LiBr layers being heated form rectangular and deep pits that open uncovered substrate areas. The edges of the pits are found to be par‐ allel to the substrate step edges ([100] and [010] directions). More effective heating enlarges the pits and rectangular patterns of nanobelts are formed. The average height of such belts is significantly larger than the initial thickness of the film indicating massive rearrangement of the deposited LiBr. The results give evidence of epitaxial growth of LiBr on the LiF(100) surface and clearly show that the LiBr adlayer orientation is intact with the substrate (i.e. the [100] LiBr axis is parallel to the substrate LiF [100] axis). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The characterization of InN growth under high‐pressure CVD conditions
Authors: Dietz N. , Alevli M. , Woods V. , Strassburg M. , Kang H. , Ferguson I. T.
Published: October 2005

Gaining insight into the gas phase and surface chemistry processes that govern the growth of InN and indium‐rich group III‐nitrides alloys is of crucial importance for understanding and controlling their materials properties. High‐pressure chemical vapor deposition (HPCVD) has been shown to be a valuable method for achieving this goal. First results show that InN layers can be grown under HPCVD conditions at 850–900 °C in the laminar flow regime of the HPCVD reactor at pressures around 15 bar and ammonia to TMI precursor flow ratio below 200. This is a major step towards the growth of indium rich group III‐nitride heterostructures due to the close processing windows. The ex situ InN layers analysis shows that the absorption edge in the InN depends strongly on the precursor flow ratio, indicating that the debated InN properties are strongly influenced by the indium‐to‐nitrogen stoichiometry. By controlling the InN point defect chemistry we showed that the absorption edge shifts from 1.8 eV down to 0.7 eV. The results show a close relation between absorption edge shift in InN and In–N stoichiometry. In order to study the growth under high‐pressure CVD conditions, real‐time optical characterization techniques have been developed and applied to analyze gas phase constituents as well as the film nucleation and steady state growth at elevated pressures. Principal angle reflection and laser light scattering are employed to study surface chemistry processes at a sub‐monolayer level, showing their superiority in optimizing and controlling the growth process. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum dynamics simulations of photodissociation reactions
Authors: Lasorne B. , Bacchus‐Montabonel M. C. , Vaeck N. , Desouter‐Lecomte M.
Published: October 2005

Wave packet simulations using ab initio potential energy surfaces (PES) have been developed within the framework of the constrained Hamiltonian methodology. The approach is presented with the example of bromoacetyl chloride photodissociation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Reactions of methyllithium with CO and CNMe: Theoretical study
Authors: Tacke Matthias , Leyden Rosaria , Cuffe Laurence P.
Published: October 2005

Hexameric methyllithium was allowed to react with carbon monoxide (or isonitrile) to form a main group metal carbonyl in the first reaction step. The species rearranges to a lithium acetyl via formal insertion of CO into the lithium carbon bond. In a further step, it is seen that a substituted ethane is formed, probably through the formation of an oxycarbene intermediate. The results of density functional theory (DFT) calculations at the B3LYP/6‐31G** level are compared with spectroscopic results, which show the existence of lithium carbonyl and acetyl species (as well as their isonitrile counterparts) at low temperature. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Reaction of trimethylsilylketene with HCl: Mechanistic study
Authors: Gaudel‐Siri Anouk , Pons Jean‐Marc , Piétri Nathalie , Tamburelli‐Couturier Isabelle , Aycard Jean‐Pierre
Published: October 2005

Ketenes are involved in various important reactions, such as [2+2] cycloadditions or nucleophilic additions. Among them, silylketenes are particularly stable, and their reactivity reveals interesting features. Indeed, they can behave as nucleophiles or electrophiles. Recent experimental results in our laboratory showed that trimethylsilylketene 1 can react with hydrogen chloride at room temperature, leading to the cleavage of the SiC bond of the ketene moiety and the formation of trimethylsilylchloride 4 and acetylchloride 5. To propose a reaction profile for this unexpected result, a theoretical study was carried out at the density functional theory (DFT) level. This mechanistic study was supported by a spectroscopic analysis in a cryogenic argon matrix in order to monitor the reaction. Intermediate 2 was then identified, and we accounted for it in the postulated reaction pathways. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Extraction of shape‐consistent spin‐orbit pseudo‐potential from an effective spin‐orbit parameter and application to the tellurium atom
Authors: Fromager Emmanuel , Teichteil Christian , Maron Laurent
Published: October 2005

A hybrid procedure to extract spin‐orbit pseudo‐potentials is proposed, taking information from both the orbital shape in the valence region and the atomic spin‐orbit splitting. An effective atomic spin‐orbit parameter is derived from a Dirac–Coulomb–Fock reference atomic calculation and is then used to extract the spin‐orbit pseudo‐potential. This method is tested for the ground‐state configuration (5s25p4) of the tellurium atom. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Nanometer‐Scale Modification and Welding of Silicon and Metallic Nanowires with a High‐Intensity Electron Beam
Authors: Xu Shengyong , Tian Mingliang , Wang Jinguo , Xu Jian , Redwing Joan M. , Chan Moses H. W.
Published: October 2005

We demonstrate that a high‐intensity electron beam can be applied to create holes, gaps, and other patterns of atomic and nanometer dimensions on a single nanowire, to weld individual nanowires to form metal–metal or metal–semiconductor junctions, and to remove the oxide shell from a crystalline nanowire. In single‐crystalline Si nanowires, the beam induces instant local vaporization and local amorphization. In metallic Au, Ag, Cu, and Sn nanowires, the beam induces rapid local surface melting and enhanced surface diffusion, in addition to local vaporization. These studies open up a novel approach for patterning and connecting nanomaterials in devices and circuits at the nanometer scale.
Spherical harmonics expansion of the Vlasov‐Poisson initial boundary value problem
Authors: Dogbe C.
Published: October 2005

We derive and analyze the 'SHE' (Spherical Harmonics Expansion) type system of equations coupled in energy. We also show that diffusive behavior occurs on long time and distance scales and we determine the diffusion tensor. The analysis is based on the governing kinetic equations arising in electron transport in semiconductors.
Knowledge of birds and willingness to support their conservation: an Australian case study
Authors: WILSON CLEVO , TISDELL CLEM
Published: October 2005

This case study concentrates on the extent of knowledge among the Australian public of Australia's tropical bird species, and their willingness to support their conservation. In order to place this issue in context, we provide background information on the status of Australian bird species, focusing attention on species that occur in tropical Australia. Then, using questionnaire survey results, we consider the hypothesis that the public's support for the conservation of different bird species depends on their understanding of the species' existence and status. Based on results from a sample of residents in Brisbane, Queensland, we found that knowledge of bird species that occur exclusively in the Australian tropics (including tropical Queensland) was very poor compared with that of those occurring in the Brisbane area that are relatively common. Experimental results indicated that when respondents in the sample had an option to allocate A$1,000 between 10 bird species listed in the survey, they allocated more funds to the better-known and more common species, unless they were provided with balanced information about all the selected species. With balanced information, the average allocation to bird species confined mostly to the Australian tropics, particularly those threatened, increased. This demonstrates the conservation implications of information provision about bird species. The results showed that public education can play a crucial role in attempts to conserve bird species that are poorly known and threatened.
Population densities and habitat associations of the range-restricted Rock Firefinch Lagonosticta sanguinodorsalis on the Jos Plateau, Nigeria
Authors: WRIGHT DAVID , JONES PETER
Published: October 2005

Population densities, using distance sampling, and habitat associations of the range-restricted Rock Firefinch Lagonosticta sanguinodorsalis were investigated between late May and early July 2002 in a protected site at Amurum on the Jos Plateau, Nigeria, and in unprotected surrounding habitats. Rock Firefinches were strongly associated with inselbergs and rocky outcrops and avoided scrub and abandoned farmland. Density was not significantly higher on the Amurum protected site (0.79 birds/ha; 95% CL 0.51–1.21) than on the unprotected areas (0.55 birds/ha; 95% CL 0.37–0.82). Rock Firefinches were locally common around inselbergs on the Jos Plateau, even where this habitat was unprotected. It remains uncertain to what extent increasing habitat degradation may affect this species' ability to persist as small populations in isolated habitat fragments. Rock Firefinch's host-specific brood parasite, the similarly range-restricted Jos Plateau Indigobird Vidua maryae, was not seen until June during this study, and no density estimate is available.
Low productivity in the Critically Endangered Mauritius Olive White-eye Zosterops chloronothos
Authors: NICHOLS RINA K. , WOOLAVER LANCE G. , JONES CARL G.
Published: October 2005

Productivity of the endemic Mauritius Olive White-eye Zosterops chloronothos, the least known of the Mauritian land-bird species, was studied for three consecutive breeding seasons. Fifteen White-eye territories were monitored in 1998–1999 and 1999–2000, and 18 in 2000–2001. Although respectively 67%, 73% and 78% of pairs in these territories exhibited signs of breeding, the annual proportion of pairs that successfully produced a fledgling was found to be extremely low at 7%, 7% and 17% respectively. Only five fledglings were observed during the 3 year period. None of the pairs was observed to have more than one successful nesting episode per season, and no pair produced more than a single fledgling over the 3 years. The extremely low productivity of this declining population is of critical concern. Species-specific conservation management is urgently required for this species.