bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III
Authors: Bork Peer , Ouzounis Christos , Sander Chris , Scharf Michael , Schneider Reinhard , Sonnhammer Erik 
Published: February 2009

AbstractWith the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S.G., et al., 1992, Nature 357, 38–46). We have tested the predictive power of computer sequence analysis on the 176 probable protein products of this chromosome, after exclusion of six problem cases. When the results of database similarity searches are pooled with prior knowledge, a likely function can be assigned to 42% of the proteins, and a predicted three‐dimensional structure to a third of these (14% of the total). The function of the remaining 58% remains to be determined. Of these, about one‐third have one or more probable transmembrane segments. Among the most interesting proteins with predicted functions are a new member of the type X polymerase family, a transcription factor with an N‐terminal DNA‐binding domain related to GAL4, a “fork head” DNA‐binding domain previously known only in Drosophila and in mammals, and a putative methyltransferase. Our analysis increased the number of known significant sequence similarities on chromosome III by 13, to now 67. Although the near 40% success rate of identifying unknown protein function by sequence analysis is surprisingly high, the information gap between known protein sequences and unknown function is expected to widen and become a major bottleneck of genome projects in the near future. Based on the experience gained in this test study, we suggest that the development of an automated computer workbench for protein sequence analysis must be an important item in genome projects.
Characterization of the stabilizing effect of point mutations of pyruvate oxidase from lactobacillus plantarum: Protection of the native state by modulating coenzyme binding and subunit interaction
Authors: Risse Bernhard , Stempfer Günter , Rudolph Rainer , Schumacher Günter , Jaenicke Rainer 
Published: February 2009

AbstractPoint mutations in the gene of pyruvate oxidase from Lactobacillus plantarum, with proline residue 178 changed to serine, serine 188 to asparagine, and alanine 458 to valine, as well as a combination of the three single point mutations, lead to a significant functional stabilization of the protein. The enzyme is a tetrameric flavoprotein with tightly bound cofactors, FAD, TPP, and divalent metal ions. Thus, stabilization may be achieved either at the level of tertiary or quaternary interactions, or by enhanced cofactor binding. In order to discriminate between these alternatives, unfolding, dissociation, and cofactor binding of the mutant proteins were analyzed. The point mutations do not affect the secondary and tertiary structure, as determined by circular dichroism and protein fluorescence. Similarly, the amino acid substitutions neither modulate the enzymatic properties of the mutant proteins nor do they stabilize the structural stability of the apoenzymes. This holds true for both the local and the global structure with unfolding transitions around 2.5 M and 5 M urea, respectively. On the other hand, deactivation of the holoenzyme (by urea or temperature) is significantly decreased.The most important stabilizing effect is caused by the Ala‐Val exchange in the C‐terminal domain of the molecule. Its contribution is close to the value observed for the triple mutant, which exhibits maximum stability, with a shift in the thermal transition of ca. 10 °C. The effects of the point mutations on FAD binding and subunit association are interconnected. Because FAD binding is linked to oligomerization, the stability of the mutant apoenzyme‐FAD complexes is increased. Accordingly, mutants with maximum apparent FAD binding exhibit maximum stability. Analysis of the quaternary structure of the mutant enzymes in the absence and in the presence of coenzymes gives clear evidence that both improved ligand binding and subunit interactions contribute to the observed thermal stabilization.
A structural model for the nucleotide binding domains of the flavocytochrome b–245 β‐chain
Authors: Taylor William R. , Jones David T. , Segal Anthony W. 
Published: February 2009

AbstractNADPH is a system in phagocytic cells that generates O2− and hydrogen peroxide in the endocytic vacuole, both of which are important for killing of the engulfed microbe. Dysfunction of this oxidase results in the syndrome of chronic granulomatous disease, characterized by a profound predisposition to bacterial and fungal infections. A flavocytochrome b is the site of most of the mutations causing this syndrome. The FAD and NADPH binding sites have been located on the β subunit of this molecule, the C‐terminal half of which showed weak sequence similarity to other reductases, including the ferredoxin‐NADP reductase (FNR) of known structure. This enabled us to build a model of the nucleotide binding domains of the flavocytochrome using this structure as a template. The model was built initially using a novel automatic modeling method based on distance–matrix projection and then refined using energy minimization with appropriate side‐chain torsional constraints. The resulting model rationalized much of the observed sequence conservation and identified a large insertion as a potential regulatory domain. It confirms the inclusion of the neutrophil flavocytochrome b‐245 (Cb‐245) as a member of the FNR family of reductases and strongly supports its function as the proximal electron transporting component of the NADPH oxidase.
Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape
Authors: Street Timothy O. , Barrick Doug 
Published: February 2009

AbstractThe Notch ankyrin domain is a repeat protein whose folding has been characterized through equilibrium and kinetic measurements. In previous work, equilibrium folding free energies of truncated constructs were used to generate an experimentally determined folding energy landscape (Mello and Barrick, Proc Natl Acad Sci USA 2004;101:14102–14107). Here, this folding energy landscape is used to parameterize a kinetic model in which local transition probabilities between partly folded states are based on energy values from the landscape. The landscape‐based model correctly predicts highly diverse experimentally determined folding kinetics of the Notch ankyrin domain and sequence variants. These predictions include monophasic folding and biphasic unfolding, curvature in the unfolding limb of the chevron plot, population of a transient unfolding intermediate, relative folding rates of 19 variants spanning three orders of magnitude, and a change in the folding pathway that results from C‐terminal stabilization. These findings indicate that the folding pathway(s) of the Notch ankyrin domain are thermodynamically selected: the primary determinants of kinetic behavior can be simply deduced from the local stability of individual repeats.
Investigation of the chromium ions recharging kinetics in Cr,Mg:YAG crystal during high‐temperature annealing
Authors: Ubizskii S. , Buryy O. , Börger A. , Becker K.‐D. 
Published: February 2009

AbstractThe optical absorption spectra of Cr,Mg:YAG crystals are studied at in‐situ conditions during high‐temperature annealing in reducing and oxidizing atmospheres. The spectra in the visible and near‐infrared regions are measured at temperatures up to 1200 °C. The kinetics of the recharging of chromium ions are studied in the temperature range between 800 °C and 1200 °C and described by mathematical models. The parameters of these models are determined from experimental kinetic curves. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
UV imaging based on AlGaN arrays
Authors: Duboz Jean‐Yves , Brault Julien , Truffer Jean‐Patrick , Robot Jean‐Alexandre , Robin Kristelle , Reverchon Jean Luc 
Published: February 2009

AbstractAlGaN Schottky photodiode arrays have been fabricated and hybridized to a commercial Si read out circuit. The array has been characterized in terms of current, spatial and temporal noise, and spectral responsivity. The array sensitivity was compared to the one expected from the performance of individual pixels, leading to the conclusion that the sensitivity of the array is currently limited by the read out circuit. Images are demonstrated with various arrays fabricated with different cut off wavelengths from 360 to 290 nm. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
HEMT‐compatible lateral field‐effect rectifier using CF4 plasma treatment
Authors: Chen Wanjun , Wong King‐Yuen , Chenr Kevin J. 
Published: February 2009

AbstractA HEMT‐compatible power lateral field effect rectifier (L‐FER) is reported and fabricated using the CF4 plasma treatment on a GaN‐on‐Si wafer. The power rectifier features a Schottky‐gate‐controlled two‐dimensional electron gas (2DEG) channel between the cathode and anode. By tying up the Schottky gate and anode together, the forward turn‐on voltage (VF, ON) of the rectifier is determined by the threshold voltage of the channel instead of the Schottky barrier. The L‐FER with a drift length of 15 μm features a VF, ON of 0.78 V at a current density of 100 A/cm2. This device also exhibits a reverse breakdown voltage (BV) of 460 V at a current level of 1mA/mm and a specific on‐resistance (RON, sp) of 2.3 mΩ·cm2, yielding a figure‐of‐merit (BV2/RON, sp) of 92 MW/cm2. The high temperature characteristics of the L‐FER are also investigated. The measurement results show a robust high temperature operation up to 250 °C. The excellent device performances, together with the lateral device structure and process compatibility with AlGaN/GaN HEMT, provide a low‐cost solution for GaN power integrated circuits. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improvement of crystalline quality of InGaN epilayers on various crystal planes of ZnO substrate by metal‐organic vapor phase epitaxy
Authors: Kawai Yohjiro , Ohsuka Shinya , Iwaya Motoaki , Kamiyama Satoshi , Amano Hiroshi , Akasaki Isamu 
Published: February 2009

AbstractWe demonstrated InxGa1‐xN epitaxial growth with InN mole fractions of x = 0.10 to 0.23 on an m‐plane ZnO substrate by metal‐organic vapor phase epitaxy. The crystalline quality of the epilayers was found to be much higher than that of epilayers grown on a GaN template on an m‐plane SiC substrate. The strain of the epilayers was investigated by X‐ray reciprocal space mapping. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Towards green lasing: ingredients for a green laser diode based on GaInN
Authors: Dräger A. D. , Jönen H. , Bremers H. , Rossow U. , Demolon P. , Schenk H. P. D. , Duboz J. Y. , Corbett B. , Hangleiter A. 
Published: February 2009

AbstractLaser structures based on GaInN quantum wells were investigated using the variable stripe length technique. Two major problems in designing a green emitting laser diode were identified. The first one is the decrease of the optical confinement for increasing wavelength. To avoid this limitation and to simultaneously maintain good optical confinement we grew samples with lattice‐matched AlInN lower cladding layers.The second major issue is to push the emission of the structures to longer wavelength by increasing the indium concentration in the quantum well. We demonstrate optical gain up to a wavelength of 480 nm (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preparation and characterization of QDs all ‐silicon
Authors: Giovannozzi Andrea M. , Rocchia Massimiliano , Troia Adriano , Bertinetti Luca , Amato Giampiero 
Published: February 2009

AbstractQuantum Dots (QDs) all‐ silicon have been prepared through ultrasound treatments of light‐emitting porous silicon layers (PSL) obtained from electrochemically etching of a p type crystalline silicon (c‐Si). The sonication treatments enabled to separate the PS nanoparticles (porousfraction) from the bulk c‐Si as well as to mechanically reduce their dimensions. The ultrasounds processes have been carried out in two different organic solvents (toluene and tetrahydrofurane, THF) which enabled us to obtaine silicon QD emitting light in the blue‐green part of the visible spectrum (estimated QDs dimension below 4nm). Moreover, by adding the proper chemicals in the solvents, such as alkenes or ω‐carboxy alkenes, we have stabilized the QDs achieving surface modification together with size reduction. Photoluminescence spectra of the QDs and TEM images will be presented in this paper. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SERS‐active substrates based on silvered porous silicon
Authors: Giorgis Fabrizio , Virga Alessandro , Descrovi Emiliano , Chiodoni Angelica , Rivolo Paola , Venturello Alberto , Geobaldo Francesco 
Published: February 2009

AbstractSilver nanoparticles are obtained through immersion plating of porous Si in AgNO3 solutions and thermal decomposition of Ag nitrate in oxidized pSi. The efficiency of nanostructures as Surface Enhanced Raman Scattering substrates is checked on a Cyanine dye evidencing detectable concentrations as low as 10–7 M. The substrate efficiency is strictly related to the Ag particle morphology, which could yield to either Localized Surface Plasmons coupled to individual particles or to inter‐particle short‐range interaction. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of a biased conductive mask on porous silicon formation
Authors: Oisten Michael K. , Bergstrom Paul L. 
Published: February 2009

AbstractPatterned macro porous p ‐type silicon has been produced using a conductive chromium and gold mask while the masking layers were electrically biased under a variety of conditions. The purpose of this work is to study the impact on pore formation near the mask edge by the modulation of the electric field orientation adjacent to the mask edge. The goal is to minimize the amount of lateral pore growth at the mask edge. The masking layers were biased at potentials between the anode and cathode potential during electrochemical anodization in an ethanoic hydrofluoric acid solution. Process conditions were defined to transfer a fraction of the total current from the sample substrate to the cathode, effectively controlling the current density in the mask, and control the electric field orientation near the mask edge. The mask bias impacted the etch rate and the profile of the pore growth at the mask edge. It was observed that if the mask was biased with respect to the anode, the impact on the porous silicon profile at the mask edge was greater than with other biasing configurations. It was observed also that the etch rate of the chromium masking layer was accelerated while biasing with respect to the cathode at a constant current density. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Decoherence of intramolecular vibrational entanglement in polyatomic molecules
Authors: Mishima K. , Yamashita K. 
Published: February 2009

AbstractThe decoherence is one of the most crucial obstacles for quantum computing, entanglement, and quantum information science, as, for example, the quantum computing is usually processed in pure state. Therefore, from the chemical interest, it is very important to investigate one of the most important decoherence mechanisms of molecules, intramolecular vibrational redistribution (IVR), from the viewpoint of quantum computing and entanglement in detail. We have found that the molecules well described by local mode picture is more suitable to maintain coherence than those well described by normal mode picture for quantum computing if the vibrational modes of polyatomic molecules are utilized for qubits. A representative light–heavy–light molecule that can be well described by local mode picture, water molecule (H2O), is adopted for calculation examples and discussion. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Characterization of polyphenol compounds from the roots and stems of Parthenocissus laetevirens by high‐performance liquid chromatography/tandem mass spectrometry
Authors: Chen Juanjuan , He Shan , Mao Hui , Sun Cuirong , Pan Yuanjiang 
Published: February 2009

AbstractA facile method based on high‐performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (HPLC/(–)ESI‐MSn) has been established for the analyses of polyphenol compounds in the root and stems of Parthenocissus laetevirens. Two characteristic fragments [C3O2 (68 Da) and C2H2O (42 Da)] were utilized for the structural identification of polyphenols. Based on the reference standards, the fragment C3O2 was presented when the compound possessed a 2,3‐dihydro‐1H‐indene‐4, 6‐diol moiety. Meanwhile, the C2H2O fragment (42 Da) yielded from the resorcinol ring was confirmed by resveratrol and three synthesized compounds identified as (E)‐5‐styrylbenzene‐1,3‐diol, (E)‐4‐styrylphenol and (E)‐4‐(3,4,5‐trimethoxystyryl)phenol. FTICR‐MSn was performed to further confirm the structures of the fragments. Overall, 15 polyphenol compounds were characterized. Three polyphenol compounds were initially and tentatively characterized from P. laetevirens for the first time, and one was proposed as a novel compound. Furthermore, a pair of stereoisomers was readily distinguished by breakdown curves, and the trans‐, cis‐isomers could be identified by HPLC/DAD‐UV spectra. Copyright © 2009 John Wiley & Sons, Ltd.
Affinity capture using chimeric membrane proteins bound to magnetic beads for rapid ligand screening by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Legros Christian , Guette Catherine , Martin‐Eauclaire Marie‐France , Goyffon Max , Tortajada Jeanine 
Published: February 2009

AbstractThe rapid and specific detection of therapeutically important ligands in complex mixtures, that may bind to membrane proteins, remains challenging for many research laboratories and pharmaceutical industries. Through its use in the development of screening assays, mass spectrometry (MS) is currently experiencing a period of tremendous expansion. In the study presented here, we took advantage of the remarkable stability properties of a bacterial membrane protein, the KcsA K+channel, produced inE.coliand purified as a tetrameric protein in the presence of a detergent. This membrane protein can subserve as a molecular template to display the pore‐forming region of human K+channels, which are considered as targets in the search for inhibitory ligands. The engineered chimeric proteins were linked to metal‐bound magnetic beads, for the screening of complex peptide mixtures, such as that of scorpion venoms. The affinity‐captured scorpion toxins were eluted prior to matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS), and to nano‐electrospray ionization tandem mass QqTOF mass spectrometry (MS/MS) analysis. Thede novosequence of the toxins was deduced by combining the MS/MS fragmentation of the reduced form (up to the 33 first residues) and the trypsin digest peptides of the native toxins. This affinity‐capture screening assay led to the isolation and characterization of potent and specific ligands of the human K+channel, Kv1.3. The affinity‐capture procedure is fast and reproducible. When linked to magnetic beads, the chimeric membrane protein can be re‐used several times without losing any of its selectivity or specificity. This assay also benefits from the fact that it requires minimal amounts of animal venoms or complex mixtures, which can be expensive or difficult to procure. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis and Characterisation of Rare Earth Complexes Supported by para‐Substituted Cinnamate Ligands
Authors: Deacon Glen B. , Forsyth Maria , Junk Peter C. , Leary Stuart G. , Lee Winnie W. 
Published: February 2009

AbstractThe preparations and characterisations of a range of lanthanoid 4‐(R)‐substituted (4‐Rcinn, R = OH, OMe, NO2, Cl), known to have good anticorrosion properties, are reported. The crystal structure of [Ce(4‐OHcinn)3(MeOH)2(H2O)]·MeOH is a polymer, in which the cerium atoms are nonacoordinate, and adjacent cerium atoms are bridged by either two bridging bidentate or two bridging tridentate carboxylate ligands. Each cerium atom also has one monodentate 4‐hydroxycinnamate ligand, one aqua ligand, and two methanol ligands.
Plasma Lipid Transfer Enzymes in Non‐Diabetic Lean and Obese Men and Women
Authors: Magkos Faidon , Mohammed B. S. , Mittendorfer Bettina 
Published: February 2009

AbstractThere are considerable differences in the plasma lipid profile between lean and obese individuals and between men and women. Little, however, is known regarding the effects of obesity and sex on the plasma concentration of enzymes involved in intravascular lipid remodeling. Therefore, we measured the immunoreactive protein mass of lipoprotein lipase (LPL), hepatic lipase (HL), cholesterol‐ester transfer protein (CETP) and lecithin‐cholesterol acyl transferase (LCAT) in fasting plasma samples from 40 lean and 40 obese non‐diabetic men and premenopausal women. Women, compared with men, had ~5% lower plasma LCAT (p < 0.041), ~35% greater LPL (p = 0.001) and ~10% greater CETP (p = 0.085) concentrations. Obese, compared with lean individuals of both sexes, had ~30% greater plasma LCAT (p < 0.001), ~20% greater CETP (p < 0.001) and ~20% greater LPL (p = 0.071) concentrations. Plasma HL concentration was not different in lean men and women. Obesity was associated with increased (by ~50%) plasma HL concentration in men (p = 0.018) but not in women; consequently, plasma HL concentration was lower in obese women than obese men (p = 0.009). In addition, there were direct correlations between plasma lipid transfer enzyme concentrations and lipoprotein particle concentrations and sizes. There are considerable differences in basal plasma lipid transfer enzyme concentrations between lean and obese subjects and between men and women, which may be partly responsible for respective differences in the plasma lipid profile.
Do Surgical Personnel Really Need to Double‐Glove?
Authors: Thomas‐Copeland Janet 
Published: February 2009

ABSTRACTIn 2007, AORN's Recommended Practices Task Force revised the “Recommended practices on prevention of transmissible infections in the perioperative practice setting” to recommend that health care practitioners double‐glove during invasive procedures. Previously, AORN had suggested that wearing two pairs of gloves might be indicated for some procedures.Research on the protective effects of double gloving provides compelling evidence that surgical personnel should double‐glove during all surgical procedures. Statistics on unreported injuries and conversion rates of HIV and hepatitis B indicate that change is difficult; however, research also suggests that objections to double‐gloving can be overcome and a practice change implemented to ensure the safety of health care workers and patients alike. AORN J 89 (February 2009) 322–328. © AORN, Inc, 2009.
NEW CHARACTERIZATIONS OF THE MEROMORPHIC BESOV, Qp AND RELATED CLASSES
Authors: AULASKARI R. , MAKHMUTOV S. , RÄTTYÄ J. 
Published: February 2009

AbstractFunctions in the meromorphic Besov, Qp and related classes are characterized in terms of double integrals of certain oscillation quantities involving chordal distances. Some of the results are analogous to the corresponding results in the analytic case.
A REVISED DUALITY PROOF OF SAMPLING LOCALIZATION IN RELAXATION SPECTRUM RECOVERY
Authors: LOY R. J. , DAVIES A. R. , ANDERSSEN R. S. 
Published: February 2009

AbstractThe duality proof of sampling localization given by Loy, Newbury, Anderssen and Davies in 2001 contains an oversight, as the classes of functions chosen do not assume the compact support. Here, it is shown how a minor change to the argument there yields a precise conclusion.