bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
Authors: Adamski Marcin , Blackwell Thomas , Menon Rajasree , Martens Lennart , Hermjakob Henning , Taylor Chris , Omenn Gilbert S. , States David J. 
Published: August 2005

AbstractThe pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and dissemination of findings from participating organizations world‐wide. Accomplishing this task required a communication and coordination infrastructure specific enough to support meaningful integration of results from all participants, but flexible enough to react to changing requirements and new insights gained during the course of the project and to allow participants with varying informatics capabilities to contribute. Challenges included integrating heterogeneous data, reducing redundant information to minimal identification sets, and data annotation. Our data integration workflow assembles a minimal and representative set of protein identifications, which account for the contributed data. It accommodates incomplete concordance of results from different laboratories, ambiguity and redundancy in contributed identifications, and redundancy in the protein sequence databases. Recommendations of the PPP for future large‐scale proteomics endeavors are described.
Synthesis and properties of new poly(terfluorene) derivatives containing spirobifluorene and electron transport groups for stable blue electroluminescence
Authors: Huang Bing , Li Jun , Chen Lianqing , Qin Jingui , Di Chong'an , Yu Gui , Liu Yunqi 
Published: August 2005

AbstractWe have synthesized three new blue‐emitting poly(terfluorene) derivatives containing spirobifluorene and electron transport groups (quinoline or oxadiazole). The strategy is to connect the monomers via positions 2 and 2′ of spirobifluorene, which significantly restricts the interchain interaction and effectively adjusts the conjugation length. The incorporation of electron‐deficient units (quinoline or oxadiazole) into the positions 7 and 7′ of spirobifluorene tunes the emission band and reduces the lowest unoccupied molecular orbital energy level. Blue electroluminescence with narrow emission was achieved in the devices of ITO/PEDOT/polymer/Ca/Al. The maximum luminances are in the range of 102–235 cd/m2 and the maximum photometric efficiencies are in the range of 0.17–0.21 cd/A. All the polymers show good spectral stability, and are promising for use as stable blue‐emitting or electron‐transport/injection materials in polymeric light‐emitting diodes. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4517–4529, 2005
Synthesis, characterization, and hyperpolarizability measurements of main‐chain azobenzene molecules
Authors: Smitha P. , Asha S. K. , Pillai C. K. S. 
Published: August 2005

AbstractA series of new AB type azobenzene monomers based on various substituted phenols and higher order fused/extended aromatic rings were synthesized and their hyperpolarizability tensor β determined by hyper‐Rayleigh scattering (HRS) measurement in methanol. The electron donor (OH) and acceptor units (COOH) were kept constant in the series, but the effective conjugation length was varied by varying the number and position of substituents as well as the number of aromatic rings. The effect of substitution of the phenolic ring on the β value was investigated and it was found to range from 15 × 10−30 to 42 × 10−30 esu. The effect of intramolecular hydrogen bonding on the nonlinear optical (NLO) property was also examined. The nonlinearity was in the following order of phenol derivative: α‐naphthol > phenyl phenol > 2,6‐dimethyl phenol > o‐cresol > cardanol > phenol > β‐naphthol. The unusually low values for the β‐naphthol‐based chromophore compared with its isomer (α‐naphthol) could be rationalized based on hydrogen bonding of the o‐hydroxyl group with the β nitrogen of the azo bridge. These azobenzene NLO chromophoric monomers were polymerized to form main‐chain polymers with a head to tail structure. The polymers had high thermal stability and rather low solubility in common organic solvents. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4455–4468, 2005
α‐α linking motifs and interhelical orientations
Authors: Engel Donald E. , DeGrado William F. 
Published: August 2005

AbstractWhile the geometry and sequence preferences of turns that link two β‐strands have been exhaustively explored, the corresponding preferences for sequences that link helical structures have been less well studied. Here we examine the interhelical geometry of two connected helices as a function of their link's length. The interhelical geometry of a helical pair appears to be significantly influenced by the number of linking residues. Furthermore, for relatively short link lengths, a very limited number of predominant conformations are observed, which can be categorized by their ϕ/ψ angles. No more than two predominant linking backbone conformations are observed for a given link length, and some linking backbone conformations correlate strongly with distinctive interhelical geometric parameters. In this study, sequence and hydrogen‐bonding patterns were defined for predominant interhelical link motifs. These results should assist in both protein structure prediction and de novo protein design. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Statistical analysis of predominantly transient protein–protein interfaces
Authors: Ansari Sam , Helms Volkhard 
Published: August 2005

AbstractA non‐redundant set of 170 protein–protein interfaces of known structure was statistically analyzed for residue and secondary‐structure compositions, pairing preferences and side‐chain–backbone interaction frequencies. By focussing mainly on transient protein–protein interfaces, the results underline previous findings for protein–protein interfaces but also show some new interesting aspects of transient interfaces. The residue compositions at interfaces found in this study correlate well with the results of other studies. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity. Secondary structure composition analysis shows that neither helices nor β‐sheets are dominantly populated at interfaces. Analyzing the pairing preferences of the secondary structure elements revealed a higher affinity within the same elements and alludes to tight packings. In addition, the results for the side‐chain and backbone interaction frequencies, which were measured under more stringent conditions, showed a high occurrence of side‐chain–backbone interactions. Taking a closer look at the helix and β‐sheet binding frequencies for a given side‐chain and backbone interaction underlined the relevance of tight packings. The polarity of interfaces increased with decreasing interface size. These types of information may be useful for scoring complexes in protein–protein docking studies or for prediction of protein–protein interfaces from the sequences alone. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Common binding site for disialyllactose and tri‐peptide in C‐fragment of tetanus neurotoxin
Authors: Jayaraman Seetharaman , Eswaramoorthy Subramaniam , Kumaran Desigan , Swaminathan Subramanyam 
Published: August 2005

AbstractClostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri‐peptide Tyr‐Glu‐Trp (YEW) have been determined to 2.3 and 2.2 Å, respectively. Both DiSia and YEW bind in a shallow cleft region on the surface of the molecule in the β‐trefoil domain, interacting with a set of common residues, Asp1147, Asp1214, Asn1216, and Arg1226. DiSia and YEW binding at the same site in tetanus toxin provides a putative site that could be occupied either by a ganglioside moiety or a peptide. Soaking experiments with a mixture of YEW and DiSia show that YEW competes with DiSia, suggesting that YEW can be used to block ganglioside binding. A comparison with the TeNT binding domain in complex with small molecules, BoNT/A and /B, provides insight into the different modes of ganglioside binding. Proteins 2005. Published 2005 Wiley‐Liss, Inc.
Thermoluminescence characterization of a MWCVD diamond film exposed to β‐rays and UV radiation
Authors: Preciado‐Flores S. , Schreck M. , Meléndrez R. , Chernov V. , Bernal R. , Cruz‐Vázquez C. , Brown F. , Barboza‐Flores M. 
Published: August 2005

AbstractThe thermoluminescence (TL) characterization of a 10 µm thick microwave plasma chemical vapor deposited (MWCVD) diamond film grown on a (001) silicon substrate and exposed to β‐rays and ultraviolet (UV) light was performed. Several TL glow peaks between 300 and 580 K as well as a highest intensity first order TL peak located at 610 K are present in the beta radiation exposed samples. UV irradiated samples exhibit mainly the 610 K TL glow peak that is fully the same to beta irradiated samples. The TL creation spectrum of UV exposed samples spans the 200–400 nm range with maximum TL efficiency around 200–230 nm and 300–380 nm. Thus, it covers the whole UV electromagnetic spectrum relevant to human health concern which is related to UV sunlight radiation reaching the Earth's surface. The TL dosimetry response is linear for beta radiation doses below 0.5 kGy. It increases sub‐linearly for higher doses. The UV exposed samples showed a linear–sub‐linear dose behavior and a high sensitivity to UV radiation for beam irradiance of the order of 10–3 W/m2. A pronounced fading of all the TL peaks was also observed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The optical absorption and photoconductivity spectra of hexagonal boron nitride single crystals
Authors: Remes Z. , Nesladek M. , Haenen K. , Watanabe K. , Taniguchi T. 
Published: August 2005

AbstractRecently, a strong cathodoluminescence at 215 nm (photon energy 5.765 eV) has been reported on pure HPHT hexagonal boron nitride (hBN) single crystals (K. Watanabe et al., Nature Mater. 3, 404 (2004)). For the first time, we measured the photocurrent and optical absorption spectra of these new hBN crystals in a broad spectral range 1–6.6 eV. Our measurements support the previously published results, especially that the single crystal hBN has a direct band gap about 5.95 eV, and a rather strong exciton binding energy that allows excitons to exist even at room temperature. We found three new opto‐electronic transitions at 2.7, 3.6 and 5.4 eV and observed the oscillatory photoconductivity in 2.7–3.6 eV region. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Detection of heavy metals in multianalyte solutions using diamond electrodes
Authors: S. Foord John , Hao Wang , Eaton Kirk 
Published: August 2005

AbstractDiamond is an attractive electrode material to replace mercury, which has been the material of choice for the electrochemical analysis of heavy metals in solution using stripping voltammetry. As a solid electrode however, interactions between different metal analytes can occur at diamond, which are not observed at Hg electrodes. We therefore examine the associated effects arising in the analysis of two types of mixed metal ion solutions, Cu–Cd and Cu–Zn, using stripping voltammetry at diamond electrodes. The detection of Cu is shown not to be strongly affected by the presence of either of the other metals, but the presence of Cu blocks the signal which otherwise would be detected for the second metal, Cd or Zn. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A structural study of model peptides derived from HIV‐1 integrase central domain
Authors: Maroun Richard G. , Zargarian Loussinée , Stocklin Reto , Troalen Frédéric , Jankowski Christopher K. , Fermandjian Serge 
Published: August 2005

AbstractThe HIV‐1 integrase (IN) catalyzes the integration of viral DNA in the human genome. In vitro the enzyme displays an equilibrium of monomers, dimers, tetramers and larger oligomers. However, its functional oligomeric form in vivo is not known. We report a study of the auto‐associative properties of three peptides denoted K156, E156 and E159. These derive from the α4 helix of the IN catalytic core. The α4 helix is an amphipatic helix exposed at the surface of the protein and could be involved in the oligomerization process through its hydrophobic face. The peptides were obtained from the replacement of several amino acid residues by more helicogenic ones in the α4 helix peptide. K156 carries the basic residues Lys156 and Lys159, which have been shown important for the binding of IN to viral DNA. In E156 and E159 they are replaced with the acidic residue Glu. A fourth peptide K(E)156 obtained from the replacement of hydrophobic residues with Glu in K156 in order to abolish the auto‐associative properties is used as a negative control. The capacity shown by peptides for α‐helical formation is demonstrated by circular dichroism (CD) analysis performed in aqueous solution and in aqueous trifluoroethanol (TFE) mixtures. Both electrospray ionization mass spectrometry (ESI‐MS) and glutaraldehyde chemical cross‐linking show that peptides adopt different solvent‐dependent equilibriums of monomers, dimers, trimers and tetramers. Oligomerization of peptides in aqueous solution is related to their ability to form helical structures. Addition of a small amount of TFE (<10%) stimulates helix stabilization and the interhelical hydrophobic contacts. Higher amounts of TFE alter the hydrophobic contacts and disrupt the oligomeric species. In addition to hydrophobic interactions, the patterns indicate that the biologically important Lys156 and Lys159 residues also participate in helix association. K(E)156 despite its ability to adopt a helical structure is unable to associate into oligomers, demonstrating the importance of hydrophobic contacts for oligomerization. Thus, the designed peptides provide us information on the functional properties of the α4 IN that seems to hold a dual role in DNA recognition and protein oligomerization. Copyright © 2005 John Wiley & Sons, Ltd.
Optimal filtering for linear systems with state and observation delays
Authors: Basin Michael , Alcorta‐Garcia Aracelia , Rodriguez‐Gonzalez Jesus 
Published: August 2005

AbstractIn this paper, the optimal filtering problem for linear systems with state and observation delays is treated proceeding from the general expression for the stochastic Ito differential of the optimal estimate, error variance, and various error covariances. As a result, the optimal estimate equation similar to the traditional Kalman–Bucy one is derived; however, it is impossible to obtain a system of the filtering equations, that is closed with respect to the only two variables, the optimal estimate and the error variance, as in the Kalman–Bucy filter. The resulting system of equations for determining the filter gain matrix consists, in the general case, of an infinite set of equations. It is however demonstrated that a finite set of the filtering equations, whose number is specified by the ratio between the current filtering horizon and the delay values, can be obtained in the particular case of equal or commensurable (τ=qh,qis natural) delays in the observation and state equations. In the example, performance of the designed optimal filter for linear systems with state and observation delays is verified against the best Kalman–Bucy filter available for linear systems without delays and two versions of the extended Kalman–Bucy filter for time delay systems. Copyright © 2005 John Wiley & Sons, Ltd.
Mechanisms of secondary ion emission from self‐assembled monolayers and multilayers
Authors: Wong Stephen C. C. , Lockyer Nicholas P. , Vickerman John C. 
Published: August 2005

AbstractAlkanethiol self‐assembled monolayers/multilayers (SAMs) have been applied as model organic systems with which to investigate secondary ion formation and emission processes during kiloelectronvolt ion bombardment. Self‐assembled monolayer and multilayer films of 11‐mercaptoundecanoic acid capped with 1‐dodecanethiol were prepared on gold‐coated substrates. Samples with varying number of thiolate layers were studied using static secondary ion mass spectrometry to investigate the origin of molecular secondary ions and the influence of surface chemistry and structure. The nature of the thiolate bonding affects the type and abundance of the observed ions. The intensity of atomic and cluster ions derived from the substrate decreases exponentially with increasing number of thiolate overlayers because of losses in transmission through the organic overlayers. Intact molecular and cluster ions can escape from >100 Å below the surface of these structures. The variation of molecular‐ion yields with multilayer thickness suggests that a significant proportion of molecular ions originate from subsurface thiolate layers. The detection of ions comprised species from the substrate or bottom of the multilayer associated with species from the top layer supports the view that chemical association at or near the surface is a viable mechanism of formation for molecular secondary ions. Copyright © 2005 John Wiley & Sons, Ltd.
A novel technique to measure the surface electrical potential of polymer films by using dielectric spectroscopy
Authors: Wang Meng‐Jiy , Tabellout M. , Chang You‐Im , Poncin‐Epaillard F. 
Published: August 2005

AbstractA novel method that allows the determination of the electrical potential of a polymer surface has been applied for polypropylene film treated by N2 + H2 cold plasma. The plasma treatment results in formation on the film surface of NH2 groups, which then gets transformed to NH3+ in contact with an electrolyte and leads to the formation of an electrical double layer. The method consists of theoretical calculation of electrical model potential, using the measurement of the electrical capacitance of the film in contact with an electrolyte by dielectric spectroscopy. Comparison with the results obtained by theoretical model shows similar dependencies of the electrical potential as a function of amino‐groups density and electrolyte concentration, but systematic differences of absolute values are observed. Copyright © 2005 John Wiley & Sons, Ltd.
Nitridation of γ‐TiAl alloys by direct metal–gas reaction at 1000–1300 K
Authors: Thongtem Somchai , Boonruang Chatdanai , Thongtem Titipun , McNallan Michael 
Published: August 2005

AbstractTwo γ‐TiAl alloys, Ti‐47at%Al‐2at%Nb‐2at%Cr (MJ12) and Ti‐47at%Al‐2at%Nb‐2at%Mn‐0.8at%TiB2 (MJ47), were nitrided by direct metal–gas reaction at 1000–1300 K in 10 cm3s−1NH3. X‐ray diffraction revealed formation of TiN at 1100–1300 K. Knoop microhardness values of the alloys were increased with an increase in the nitridation temperature. Microhardness values of MJ12 and MJ47 with 1300 K nitridation were respectively improved to 1.65 and 1.38 times those of the controls. Nitridation depth at a variety of temperature determined by Rutherford backscattering spectrometry was increased with an increase in the temperature. Ti, Al and N concentrations at a variety of depths analysed by scanning electron microscopy and energy dispersive X‐ray linescanning are also explained. Copyright © 2005 John Wiley & Sons, Ltd.
Quantitative determination of surface energy using atomic force microscopy: the case of hydrophobic/hydrophobic contact and hydrophilic/hydrophilic contact
Authors: Awada Houssein , Castelein Gilles , Brogly Maurice 
Published: August 2005

AbstractAtomic force microscopy (AFM) has been used to determine the surface energy of chemically modified surfaces at a local scale. In order to achieve this aim, it was necessary to graft both the AFM tip and the substrate with the same chemical functional groups. Two different organothiols terminated either by hydrophilic or hydrophobic chemical functionalities were used. Grafting process classically reported shows that after UV/ozone treatment for 30 min, the tip is coated by thermal deposition with 4‐5‐nm‐thick titanium layer followed by a 30‐nm‐thick gold layer. Finally, the tip is grafted by organothiols. The thickness of the layer deposited on the tip is of the same order of magnitude as the tip radius. To avoid the use of Ti and to decrease the thickness of the gold layer, we have developed a new way of grafting by using organic molecules like (3‐mercaptopropyl)triethoxysilane (MPS) as a linkage agent. Then this way of grafting was checked. Finally, AFM force‐distance curves, between grafted tips and chemically modified surface, were carried out in contact mode. Calibration of the various parts of the apparatus and especially of the cantilever (spring constant and tip radius) is of major importance to reach quantitative data. Finally, by applying a suitable theory of contact, we were able to determine the surface energy of our system. Copyright © 2005 John Wiley & Sons, Ltd.
Abortion procedures in a tertiary care institution in India
Authors: Choudhary N. , Saha S.C. , Gopalan S 
Published: August 2005

AbstractObjective: To determine the complications rate of termination of pregnancy (TOP) and the risk factors for complications following TOP. Methods: Retrospective observational study of the records of 1287 women who underwent TOP in the Department of Obstetrics and Gynaecology of the Postgraduate Institute of Medical Education and Research, Chandigarh, India, between 1997 and 2001. First‐trimester abortion was performed in 1088 women (85%) and second‐trimester abortion in 199 women (15%). Most women (76%) were aged between 26 and 30 years; they were educated and requested TOP primarily to limit the number of their children or to space their births. A malformed fetus was the indication for TOP in 5.9% cases, and 16% of the women had medical disorders associated with the pregnancy. Suction evacuation was the method of choice for first‐trimester abortion (88%); dinoprostone gel and extra‐amniotic saline solution plus oxytocin infusion were the primary methods (71%) for second‐trimester abortion. Results: Uterine perforation occurred in 1 patient (0.09%) after a first‐trimester abortion. The total rate of complications was 3.79% after first‐trimester and 4.0% after second‐trimester abortions. Excessive hemorrhage and retained placenta were chief complications associated with second‐trimester abortion. Incomplete abortion (1.5%) and minor infection were seen in 2.3% patients. The rate of complications was higher among parous women. Postabortion insertion of a CuT intrauterine device increased the need for a second course of antibiotics. Conclusion: Termination of pregnancy is safe if adequate care is taken while performing the procedure.