bluuebunny/crossref_metadata_2025_split huggingface dataset:
Will my protein crystallize? A sequence‐based predictor
Authors: Smialowski Pawel , Schmidt Thorsten , Cox Jürgen , Kirschner Andreas , Frishman Dmitrij 
Published: November 2005

AbstractWe propose a machine‐learning approach to sequence‐based prediction of protein crystallizability in which we exploit subtle differences between proteins whose structures were solved by X‐ray analysis [or by both X‐ray and nuclear magnetic resonance (NMR) spectroscopy] and those proteins whose structures were solved by NMR spectroscopy alone. Because the NMR technique is usually applied on relatively small proteins, sequence length distributions of the X‐ray and NMR datasets were adjusted to avoid predictions biased by protein size. As feature space for classification, we used frequencies of mono‐, di‐, and tripeptides represented by the original 20‐letter amino acid alphabet as well as by several reduced alphabets in which amino acids were grouped by their physicochemical and structural properties. The classification algorithm was constructed as a two‐layered structure in which the output of primary support vector machine classifiers operating on peptide frequencies was combined by a second‐level Naive Bayes classifier. Due to the application of metamethods for cost sensitivity, our method is able to handle real datasets with unbalanced class representation. An overall prediction accuracy of 67% [65% on the positive (crystallizable) and 69% on the negative (noncrystallizable) class] was achieved in a 10‐fold cross‐validation experiment, indicating that the proposed algorithm may be a valuable tool for more efficient target selection in structural genomics. A Web server for protein crystallizability prediction called SECRET is available athttp://webclu.bio.wzw.tum.de:8080/secret. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Hierarchy of equations in the generalized density functional theory
Authors: Nagy Á. 
Published: November 2005

AbstractFunctional relations and equations of hierarchy in the generalized density functional theory (DFT) are derived from coordinate scaling and adiabatic connection. Local and nonlocal solutions for the noninteracting kinetic energy, exchange energy, correlation energy, and the kinetic energy correction functionals are presented. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Treating hydrogen bonding in ab initio calculation of biopolymers
Authors: Mei Ye , Wu Emilia L. , Han K.L. , Zhang J.Z.H. 
Published: November 2005

AbstractWe present a general scheme to treat backbone hydrogen bonding in protein using the molecular fractionation with conjugate caps (MFCC) approach. In this approach, molecular caps are employed to mimic the hydrogen bonding environment of protein fragments that are calculated individually. Using this scheme in the MFCC method, we carried out explicit numerical calculations for a number of secondary structures of proteins, including the α‐helix and β‐sheet. The calculated electron densities, electrostatic potentials, and dipole moment are compared with those from the standard full system ab initio calculations. The result shows that the current treatment using the hydrogen bond cap gives an accurate description of the hydrogen bonding effect and accurate dipole moment. In contrast, calculation using the standard force field (FF) approach gives dipole moments that are in huge error (i.e., significantly smaller) than the quantum result for helix structures due to the lack of polarization effect with fixed partial charges. The present study demonstrates that the MFCC approach can quantitatively describe hydrogen bonding in practical ab initio calculation of proteins. Our result also underscores the importance of the polarization effect in backbone hydrogen bonding of protein. This could have significant implication in studying the electrostatic interaction of proteins, such as protein solvation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Computational study of maleamic acid cyclodehydration with acetic anhydride
Authors: Constantinescu Mircea , Ivanov Daniela 
Published: November 2005

AbstractThe reaction mechanisms of N‐substituted maleamic acids (MA) cyclodehydration (CDH) to the corresponding maleimides (M) and isomaleimides (IM) and IM rearrangement to M were studied by the PM3 Hamiltonian with charge model 1 (CM1P) of the AMSOL computational method with solvation effect in order to establish the most probable pathways. CDH was considered in the presence of acetic anhydride in the presence of an acetate anion or triethylamine as the dehydrating agent in CH2Cl2 as the solvent. In the first step, our computational results supported carboxylic proton losses, provided by a nucleophilic center on the dehydrating agent. In the next step, maleamic acid anion could either add a molecule of a dehydrating agent (path A) or cyclicize (path B). Our results indicate the path B to require more energy than path A, so path B is considered less likely to occur. The formation (path A) of an anion complex I2 between the anion of MA and the dehydration agent was supported as well as acetate anion loss to form the neutral mixed anhydride I3. The ring closure to M or IM occurs only after I3 amide proton loss, meaning that the dehydrating agent necessitate another nucleophilic center. The cyclization of I4 anion over amide nitrogen or oxygen to the reaction outcome depends on the electronic effect of amide nitrogen substituent. The same results were obtained studying CDH of N‐substituted ophthalmic acids with acetic anhydride and for MA with N,N′‐dicyclohexylcarbodiimide as dehydrating agent, in the same solvent. In such circumstances, one can consider them the common features of a general CDH reaction mechanism of MA. Our computational results found the IM to M rearrangement to correspond to the reversible final path of synthesis mechanism although the other investigators considered it to take place under a different reaction. They also supported the importance of the acetate anion in both cyclization and rearrangement mechanisms; the presence of tertiary amine blocks the acetic acid formed during reaction, determines I3 amide proton loss and prevents rearrangement. The theoretical conclusions are consistent with the experimental results. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
New classes of orthogonal polynomials
Authors: Srivastava Vipin , Ramesh Naidu A. 
Published: November 2005

AbstractWe show that two new classes of orthogonal polynomials can be derived by applying two orthogonalization procedures due to Löwdin to a set of monomials. They are new in that they possess novel properties in terms of their inner products with the monomials. Each class comprises sets of orthogonal polynomials that satisfy orthogonality conditions with respect to a weight function on a certain interval. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Rapid analysis of controlled substances using desorption electrospray ionization mass spectrometry
Authors: Rodriguez‐Cruz Sandra E. 
Published: November 2005

AbstractThe recently developed technique of desorption electrospray ionization (DESI) has been applied to the rapid analysis of controlled substances. Experiments have been performed using a commercial ThermoFinnigan LCQ Advantage MAX ion‐trap mass spectrometer with limited modifications. Results from the ambient sampling of licit and illicit tablets demonstrate the ability of the DESI technique to detect the main active ingredient(s) or controlled substance(s), even in the presence of other higher‐concentration components. Full‐scan mass spectrometry data provide preliminary identification by molecular weight determination, while rapid analysis using the tandem mass spectrometry (MS/MS) mode provides fragmentation data which, when compared to the laboratory‐generated ESI‐MS/MS spectral library, provide structural information and final identification of the active ingredient(s). The consecutive analysis of tablets containing different active components indicates there is no cross‐contamination or interference from tablet to tablet, demonstrating the reliability of the DESI technique for rapid sampling (one tablet/min or better). Active ingredients have been detected for tablets in which the active component represents less than 1% of the total tablet weight, demonstrating the sensitivity of the technique. The real‐time sampling of cannabis plant material is also presented. Published in 2005 by John Wiley & Sons, Ltd.
A longitudinal study of ethanol and acetaldehyde in the exhaled breath of healthy volunteers using selected‐ion flow‐tube mass spectrometry
Authors: Turner Claire , Španěl Patrik , Smith David 
Published: November 2005

AbstractSelected‐ion flow‐tube mass spectrometry (SIFT‐MS) has been used to monitor the volatile compounds in the exhaled breath of 30 volunteers (19 male, 11 female) over a 6‐month period. Volunteers provided breath samples each week between 8:45 and 13:00 (before lunch), and the concentrations of several trace compounds were obtained. In this paper the focus is on ethanol and acetaldehyde, which were simultaneously quantified by SIFT‐MS using H3O+ precursor ions. The mean ethanol level for all samples was 196 parts‐per‐billion (ppb) with a standard deviation of 244 ppb, and the range of values for breath samples analysed is 0 to 1663 ppb. The mean acetaldehyde level for all samples was 24 ppb with a standard deviation of 17 ppb, and the range of values for breath samples analysed is 0 to 104 ppb. Background (ambient air) levels of ethanol were around 50 ppb, whereas any background acetaldehyde was usually undetectable. Increased ethanol levels were observed if sweet drink/food had been consumed within the 2 h prior to providing the breath samples, but no increase was apparent when alcohol had been consumed the previous evening. The measured endogenous breath ethanol and acetaldehyde levels were not correlated. These data relating to healthy individuals are a prelude to using breath analysis for clinical diagnosis, for example, the recognition of bacterial overload in the gut (ethanol) or the possibly of detecting tumours in the body (acetaldehyde). Copyright © 2005 John Wiley & Sons, Ltd.
Exponential estimates for neutral time delay systems with multiple delays
Authors: Kharitonov Vladimir , Collado Joaquín , Mondié Sabine 
Published: November 2005

AbstractExponential estimates and sufficient conditions for the exponential stability of linear neutral time delay for systems with multiple delays are given. The case of systems with uncertainties, including uncertainties in the difference operator, is considered. The proofs follows from new results on non‐homogeneous difference equations evolving in continuous time combined with the Lyapunov–Krasovskii functionals approach. The conditions are expressed in terms of linear matrix inequalities. The particular case of neutral time delay systems with commensurate delays, which leads to less restrictive exponential estimates, is also addressed. Copyright © 2005 John Wiley & Sons, Ltd.
Finding blocks and other patterns in a random coloring of ℤ
Authors: Matzinger Heinrich , Rolles Silke W.W. 
Published: November 2005

AbstractLet ξ = (ξk)k∈ℤ be i.i.d. with P(ξk = 0) = P(ξk = 1) = 1/2, and let S: = (Sk) be a symmetric random walk with holding on ℤ, independent of ξ. We consider the scenery ξ observed along the random walk path S, namely, the process (χk := ξ). With high probability, we reconstruct the color and the length of blockn, a block in ξ of length ≥ n close to the origin, given only the observations (χk). We find stopping times that stop the random walker with high probability at particular places of the scenery, namely on blockn and in the interval [−3n,3n]. Moreover, we reconstruct with high probability a piece of ξ of length of the order 3 around blockn, given only 3 observations collected by the random walker starting on the boundary of blockn. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Directed Fabrication of Radially Stacked Multifunctional Oxide Heterostructures Using Soft Electron‐Beam Lithography
Authors: Pan Zixiao , Donthu Suresh K. , Wu Nianqiang , Li Shuyou , Dravid Vinayak P. 
Published: November 2005

AbstractA versatile patterning approach based on electron‐beam lithography (eBL) and solution deposition, termed soft‐eBL, has been developed to fabricate radially stacked heterostructures of multifunctional oxides from their sol precursors. Well‐defined nanorings of lead zirconate titanate (PZT) are fabricated on a variety of substrates such as noble metals (e.g., Au), semiconductors (e.g., Si), and oxide single crystals (e.g., SrTiO3), which were previously functionalized with appropriate self‐assembled monolayers (SAMs). The undercut in the double‐layer eBL resist and substrate functionalization with the SAM treatment play a vital role in the formation of the ring structures. The nanorings are then used as building block “containers” and ring‐reservoirs are filled with a second sol (e.g., CoFe2O4) to form radially stacked composite ceramic heterostructures. The approach presented here does not require either feature alignment to realize heterostructures or the etching of ceramics, and is amenable to a variety of radially stacked composite heterostructures.
What lies behind graphicacy? Relating students' results on a test of graphically represented quantitative information to formal academic achievement
Authors: Åberg‐Bengtsson Lisbeth , Ottosson Torgny 
Published: November 2005

AbstractBased on studies carried out on qualitative data an instrument was constructed for investigating how larger numbers of students handle graphics. This test, consisting of 18 pages, each with its own graphic display(s) and a set of tasks, was distributed to 363 students, 15–16 years of age, from five different schools. The format of the questions varied, as did the format of the graphics. As students' performance was expected to be multidimensional, confirmatory factor analysis was carried out with a structural equation modeling technique. In addition to the identification of a general graphicacy‐test factor (Gen) and an end‐of‐test effect (End′), a narrative dimension (Narr′) was vaguely indicated. This model was then related to a six‐factor model of students' formal academic achievement measured by their leaving certificates from compulsory education. The strongest correlation obtained was between the general graphicacy‐test dimension (Gen) and a mathematic/science factor (MathSc′) in the grades model. In addition, substantial relationships were detected between the Gen factor and both an overall school achievement factor (SchAch) and a language factor (Lang′) in the grades model. © 2005 Wiley Periodicals, Inc. J Res Sci Teach 43: 43–62, 2006
Inscriptional practices in two inquiry‐based classrooms: A case study of seventh graders' use of data tables and graphs
Authors: Wu Hsin‐Kai , Krajcik Joseph S. 
Published: November 2005

AbstractThis case study characterizes the inscriptional practices demonstrated by seventh graders, particularly their use of data tables and graphs, in an inquiry‐based learning environment. Using a naturalistic approach, we collected multiple sources of data during an 8‐month instructional unit that emphasized water quality and relevant concepts. The analyses show that constructing and interpreting graphs and tables provided students with opportunities to discuss, review, and clarify questions about concepts and the inquiry process. At the end of the unit on water quality, students were capable of fully participating in designing a more complicated inscription and interpreting new inscriptions. The findings suggest that four features of the learning environment promoted the development of inscriptional practices: (1) embedding the use of inscriptions in students' science inquiry; (2) providing scaffolds to support students' inquiry process; (3) sequencing tasks and the inquiry process; and (4) engaging students in science inquiry in an iterated manner. This study provides insight into the design of a learning environment in which students can develop competent scientific practices. © 2005 Wiley Periodicals, Inc. J Res Sci Teach 43: 63–95, 2006
Relationship between achievement and students' acceptance of evolution or creation in an upper‐level evolution course
Authors: Ingram Ella L. , Nelson Craig E. 
Published: November 2005

AbstractStudents often hold strong attitudes regarding topics they encounter during their studies, and many instructors feel that these attitudes can have strong effects on students' performance. We characterized students' attitudes toward evolution and investigated the influence of students' attitudes (pre‐course and post‐course) regarding evolution on their performance in an evolution course, measured as their final grade. We found our students to hold positive attitudes toward evolution; these attitudes became more positive following the course. The most significant change in attitude occurred in the group of students initially undecided toward evolution. We also found that attitudes prior to the course had little influence on later achievement; however, at the end of the course, students' attitudes were positively related to final grades, although the effect was small. We argue that pedagogical techniques directly addressing students' attitudes help reduce the influence of attitudes (especially prior attitudes) on achievement. © 2005 Wiley Periodicals, Inc. J Res Sci Teach 43: 7–24, 2006
“It isn't no slang that can be said about this stuff”: Language, identity, and appropriating science discourse
Authors: Brown Bryan A. 
Published: November 2005

AbstractThis investigation explores how underrepresented urban students made sense of their first experience with high school science. The study sought to identify how students' assimilation into the science classroom reflected their interpretation of science itself in relation to their academic identities. The primary objectives were to examine students' responses to the epistemic, behavioral, and discursive norms of the science classroom. At the completion of the academic year, 29 students were interviewed regarding their experiences in a ninth and tenth‐grade life science course. The results indicate that students experienced relative ease in appropriating the epistemic and cultural behaviors of science, whereas they expressed a great deal of difficulty in appropriating the discursive practices of science. The implications of these findings reflect the broader need to place greater emphasis on the relationship between students' identity and their scientific literacy development. © 2005 Wiley Periodicals, Inc. J Res Sci Teach 43: 96–126, 2006
Offshore wind climatology over the Mediterranean basin
Authors: Lavagnini A. , Sempreviva Anna M. , Transerici C. , Accadia C. , Casaioli M. , Mariani S. , Speranza A. 
Published: November 2005

AbstractTo obtain the offshore wind climatology over the whole Mediterranean region, European Centre for Medium‐range Weather Forecasts (ECMWF) 6‐hourly wind data over a grid resolution of 0·5° × 0·5° for a period of 24 years have been retrieved. Data sets at 850 and 700 hPa pressure levels and 10 m above the surface were downloaded. For each grid point, mean wind speeds and Weibull probability density function parameters have been computed. As the wind field of ECMWF at 10 m is less accurate near the coast and in narrow basins, e.g. the Adriatic Sea, owing to the size of the mesh and land–sea mask smoothness, these statistics have been corrected, for each grid point, with the statistics produced using 2 year runs of a limited‐area model with a grid size of 10 km. Results have been compared with experimental data from buoys, islands and ships in various regions of the basin. Maps of mean wind speeds and Weibull parameters are shown here for the whole Mediterranean Sea to illustrate these results. Copyright © 2005 John Wiley & Sons, Ltd.
Modelling and ride‐through capability of variable speed wind turbines with permanent magnet generators
Authors: Akhmatov Vladislav 
Published: November 2005

AbstractA model for a variable speed wind turbine with a permanent magnet, multipole, synchronous generator is developed and implemented in the simulation tool PSS/E as a user‐written model. The model contains representations of the permanent magnet generator, the frequency converter system with control, the aerodynamic rotor and a lumped mass representation of the shaft system. This model complexity is needed for investigations of the short‐term voltage stability and ride‐through capability of such wind turbines. Ride‐through capability is a major issue and, for the given concept, can be achieved by applying blocking and restart sequences to the frequency converter at the voltage drop in the power grid. Copyright © 2005 John Wiley & Sons, Ltd.
Study on synchronization phenomena of fixed speed wind turbines with an induction generator in a wind farm
Authors: Nanahara Toshiya , Katayama Norihide , Takata Go , Miyake Masatoshi 
Published: November 2005

AbstractSynchronization of rotor angles of fixed speed wind energy converters with an induction generator has been reported in several wind farms. In terms of impacts on a power system, the synchronization could worsen the voltage flicker problems. Although many articles have examined this synchronization, there remains considerable room in the physical interpretation of the phenomena. This article discusses the physical context of the synchronization phenomena of wind turbines in a wind farm. After analysing interaction among electric power output, voltage, generator slip and rotor angle, differential equations describing the phenomena are presented. The synchronization phenomena are examined through a study on equilibria of the equations and their stability. Fundamental characteristics of the phenomena such as pull‐in force, speed of synchronization and the impact of discrepancies among generator characteristics are discussed for two‐ and three‐machine systems. The results show that synchronization tends to occur in wind energy converters with large 3p components and a low power factor, which are interconnected into a grid with large short‐circuit impedance of high X/R ratio. Copyright © 2005 John Wiley & Sons, Ltd.