bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimally informative backbone structural propensities in proteins
Authors: Solis Armando D. , Rackovsky S. 
Published: October 2002

AbstractWe use basic ideas from information theory to extract the maximum amount of structural information available in protein sequence data. From a non‐redundant set of protein X‐ray structures, we construct local‐sequence‐dependent [ϕ,ψ] distributions that summarize the influence of local sequence on backbone conformation. These distributions, approximations of actual backbone propensities in the folded protein, have the following properties: (1) They compensate for the problem of scarce data by an optimized combination of local‐sequence‐dependent and single‐residue specific distributions; (2) They use multi‐residue information; (3) They exploit similarities in the local coding properties of amino acids by collapsing the amino acid alphabet to streamline local sequence description; (4) They are designed to contain the maximum amount of local structural information the data set allows. Our methodology is able to extract around 30 cnats of information from the protein data set out of a total 387 cnats of initial uncertainty or entropy in a finely discretized [ϕ,ψ] dihedral angle space (18 × 18 structural states), or about 7.8%. This was achieved at the hexamer length scale; shorter as well as longer fragments produce reduced information gains. The automatic clustering of amino acids into groups, a component of the optimization procedure, reveals patterns consistent with their local coding properties. While the overall information gain from local sequence is small, there are some local sequences that have significantly narrower structural distributions than others. Distribution width varies from at least 20% less than the average overall entropy to at least 14% above. This spread is an expression of the influence of local sequence on the conformational propensities of the backbone chain. The optimal ensemble of local‐sequence‐specific backbone distributions produced is useful as a guide to structural predictions from sequence, as well as a tool for further explorations of the nature of the local protein code. Proteins 2002;48:463–486. © 2002 Wiley‐Liss, Inc.
Understanding protein structure‐function relationships in Family 47 α‐1,2‐mannosidases through computational docking of ligands
Authors: Mulakala Chandrika , Reilly Peter J. 
Published: October 2002

AbstractFamily 47 α‐1,2‐mannosidases are crucial enzymes involved in N‐glycan maturation in the endoplasmic reticula and Golgi apparati of eukaryotic cells. High‐resolution crystal structures of the human and yeast endoplasmic reticulum α‐1,2‐mannosidases have been recently determined, the former complexed with the inhibitors 1‐deoxymannojirimycin and kifunensine, both of which bind in its active site in the unusual 1C4 conformation. However, unambiguous identification of the catalytic proton donor and nucleophile involved in glycoside bond hydrolysis was not possible from this structural information. In this work, α‐D‐galactose, α‐D‐glucose, and α‐D‐mannose were computationally docked in the active site in the energetically stable 4C1 conformation as well as in the 1C4 conformation to compare their interaction energetics. From these docked structures, a model for substrate and conformer selectivity based on the dimensions of the active site was proposed. α‐D‐Galactopyranosyl‐(1→2)‐α‐D‐mannopyranose, α‐D‐glucopyranosyl‐(1→2)‐α‐D‐mannopyranose, and α‐D‐mannopyranosyl‐(1→2)‐α‐D‐mannopyranose were also docked into the active site with their nonreducing‐end residues in the 1C4 and E4 (representing the transition state) conformations. Based on the docked structure of α‐D‐mannopyranosyl‐E4‐(1→2)‐α‐D‐mannopyranose, the catalytic acid and base are Glu132 and Glu435, respectively. Proteins 2002;49:125–134. © 2002 Wiley‐Liss, Inc.
Existence of strictly diabatic basis sets for the two‐state problem
Authors: Kryachko Eugene S. , Varandas António J. C. 
Published: October 2002

AbstractSome new properties of the nonadiabatic coupling elements are derived, in particular the orthogonality and gauge invariance of their longitudinal and transverse components. A method for constructing a strictly diabatic basis set that makes both the transverse and longitudinal components of the nonadiabatic coupling elements of the two‐state problem vanish identically and is based on introducing overlap between the electronic states in the vicinity of the crossing seam is proposed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Complexes of C60 fullerene with simple donor molecules: Theoretical study
Authors: Fomina Lioudmila , Reyes Abraham , Fomine Serguei 
Published: October 2002

AbstractThe complex formation between fullerene C60 and simple donor molecules such as dimethyl ether, dimethylamine, dimethylsulfide, furan, pyrrole, and thiophene has been studied applying the hybrid MP2/6‐31G(d′):PM3 ONIOM approach for geometry optimization. Local implementation of Møller–Plesset perturbation theory in combination with 6‐31G(d) and 6‐311G(d,p) basis sets was used for binding energies estimation of fullerene complexes. Two factors were found to contribute most to the complex stability: the polarizability and molecular volume of donor molecule. As follows from positive stabilization energies at the Hartree–Fock level, the stabilization of fullerene complexes is entirely due to dispersion interactions in accordance with available experimental data. The calculations show that for donors of similar molecular volume the binding energy of molecular complex increases with polarizability of donor molecules. Similarly, for such complexes the partial charges on molecules increase with decreasing of ionization potentials of donor molecules. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Mass spectrometric determination of the dissociation energy of Mn2F6(g)
Authors: Ciccioli Andrea , Rau Julietta V. , Balducci Giovanni , Brutti Sergio , Chilingarov Norbert N. , Gigli Guido , Cesaro Stella Nunziante 
Published: October 2002

AbstractThe gaseous Mn2F6 molecule has been identified for the first time in the vapor produced by MnF3 vaporization and the MnF3(g) dimerization equilibrium studied by the Knudsen cell mass spectrometry technique in the 884–1015 K temperature range. The experimental vapor pressure data were treated by the second‐ and third‐law procedures, and the enthalpy of Mn2F6(g) dissociation has been determined as: $\font\mathbfit=cmmib10\def\bfit#1{\hbox{\mathbfit #1}} {\bf \Delta {\bfit H}_{0}^{o} [Mn_{2}F_{6}(g)] = 210.9 \pm 2.5 kJ/mol}$. Thermodynamic functions of gaseous MnF3 were calculated from geometrical and vibrational parameters taken from the literature. For gaseous Mn2F6, they were evaluated by comparison with molecular parameters of Co2F6(g). Copyright © 2002 John Wiley & Sons, Ltd.
A combined ion source for fast switching between electrospray and matrix‐assisted laser desorption/ionization in Fourier transform ion cyclotron resonance mass spectrometry
Authors: Baykut Gökhan , Fuchser Jens , Witt Matthias , Weiss Gerhard , Gosteli Christoph 
Published: October 2002

AbstractA new ion source has been developed for Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) that enables quick changes between matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) modes. When operating as an ESI source, the sample solution is sprayed through an angled nebulizer. The generated ions pass through a glass capillary followed by a skimmer and three sequential hexapole ion guides. Ions can be accumulated in the third hexapole (storage hexapole) before they are injected into the ICR trap. The second hexapole is mounted on a movable platform which also carries the MALDI sample plate. During the switch from ESI to MALDI, this platform moves the second hexapole out of the hexapole series and locates a MALDI sample plate with 384 sample positions into the area directly in front of the storage hexapole. The storage hexapole is in a medium pressure chamber (MPC) which has windows both for the incoming laser beam and for the observation optics, as well as a gas tube for pulsing collision gas into the chamber. During the MALDI operation the focused laser beam enters the MPC, passes between the hexapole rods and irradiates a MALDI sample on the target plate. The sample molecules are desorbed/ionized into the storage hexapole and simultaneously cooled by collisions with the pulsed gas. Ions desorbed from multiple laser shots can be accumulated in this hexapole before they are transferred to the ICR trap. With the combined ion source a computer‐controlled switch between MALDI and ESI modes is possible in less than a minute, depending on the position of the MALDI target on the 384‐spot plate. Immediate acquisition of mass spectra is possible after mode switching without the need for tuning or re‐calibration. Copyright © 2002 John Wiley & Sons, Ltd.
New results on matrix‐assisted laser desorption/ionization mass spectrometry of widely polydisperse hydrosoluble polymers
Authors: Malvagna Paola , Impallomeni Giuseppe , Cozzolino Rosaria , Spina Emanuela , Garozzo Domenico 
Published: October 2002

AbstractPolyvinylpyrrolidone (PVP) of molecular weight (Mw) 40 000 and 160 000 and polydispersity of 1.8–2.2 was shown to yield matrix‐assisted laser desorption/ionization (MALDI) mass spectra with the correct molar mass distribution of the polymer. This is a unique behavior among widely polydisperse samples and was ascribed to the capacity of PVP to complex the MALDI matrix. This result prompted us to test a new sample preparation technique consisting of flash‐freezing followed by freeze‐drying of the solution of the polymer with the matrix. In this paper we describe our preliminary results on MALDI‐MS of polydisperse polymers obtained by this technique. This sample preparation method allowed us to obtain, for the first time, spectra yielding the true molecular weight distribution of polydisperse samples such as dextran, lichenan, nigeran, and poly(ethylene oxide). Copyright © 2002 John Wiley & Sons, Ltd.
Some properties of ion trajectories in the radial plane of an axially symmetric ion trap
Authors: Sheretov Ernst P. , Philippov Igor V. , Karnav Tatiana B. , Ivanov Vladimir W. 
Published: October 2002

AbstractIn this article we analyse the trajectories of externally generated ions injected in the radial plane into the ion trap. The shape of the envelope curves for two‐dimensional (2D) ion trajectories is determined. Conditions under which these envelope curves can be transformed into circles are found. We show that the amplitude of ion oscillations is a minimum in this case and that this mode corresponds to optimised ion trapping conditions. Also we discuss a ring‐shaped ion trap mass spectrometer electrode system which consists of two ring electrodes, and which utilises ion trajectories with circular envelope curves. Copyright © 2002 John Wiley & Sons, Ltd.
Automatic sleep stage scoring based on waveform recognition method and decision‐tree learning
Authors: Hanaoka Masaaki , Kobayashi Masaki , Yamazaki Haruaki 
Published: October 2002

AbstractThere have been many trials in which the waveform recognition method, which is intended to replace expert observation by computer processing, has been used to extract the features of biological signals during sleep, and to automatically score sleep stages based on feature parameters. This paper proposes a waveform recognition method which extracts the feature parameters based on the characteristics of the biological signal during sleep, and a method of automatic sleep stage scoring by decision‐tree learning, which is currently considered to be one of the most successful machine learning methods in practice. As the first step in the method, the features corresponding to the state of the EEG, the EOG, and the EMG during sleep are compared to the features of characteristic waves such as the α‐wave, δ‐wave, sleep spindle, K‐complex, and REM, and the feature parameters needed in order to judge the sleep stage are extracted. Using canonical discriminant analysis and discretization method RWS based on the random walk, the feature parameters are converted to a small number of discrete variables. Based on training instances, obtained by the bootstrap method, a set of multiple small decision trees (a committee) is formed, and the sleep stage is scored by majority decision in the classification results. The method is applied to the PSG chart digital data provided by the Japan Sleep Society, and the performance of the system is evaluated experimentally. It is verified that the proposed method is promising as a method of automatic sleep stage scoring with high accuracy, requiring little expenditure of time in learning and classification. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(11): 1–13, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10248
Reflectometry studies of the oxidation kinetics of thin copper films
Authors: Njeh Anouar , Wieder Thomas , Fuess Hartmut 
Published: October 2002

AbstractOxide formation on magnetron‐sputtered thin copper films (35 nm thickness) was studied by x‐ray reflectometry and grazing incidence x‐ray diffraction. The films were oxidized in air at temperatures of 175° C, 200° C, 225° C and 250° C. The reflectometry and the diffractometry data indicate the formation of Cu2O. A power‐law dependence of the oxide layer thickness was found. The activation energy obtained is weakly time dependent. Copyright © 2002 John Wiley & Sons, Ltd.
How to develop and to reuse the UniPDM framework
Authors: Kim Jeong Ah 
Published: October 2002

AbstractReuse through frameworks promises improved productivity and reduced learning curves across the enterprise. Although many enterprise framework projects have commenced, few real enterprise frameworks have achieved noteworthy success. Our research with enterprise frameworks focuses on product data management. In this paper we focus on the current state and the findings of our project. Through our efforts we believe we have identified some important lessons for teams involved in enterprise framework development. Our discussion will concentrate on the following: (1) the phases of developing our framework; (2) applying the design pattern; (3) supporting environments for customizing the framework; (4) the problems in developing a framework. Copyright © 2002 John Wiley & Sons, Ltd.
Enterprise frameworks for workflow management systems
Authors: Gimenes Itana M. S. , Barroca Leonor 
Published: October 2002

AbstractThis paper proposes an enterprise framework for workflow management (WFM) systems based on the Workflow Management Coalition generic architecture. In addition, it presents one smaller object‐oriented framework for task scheduling. This framework is obtained by refining one of the packages of the overall framework. The task scheduling framework was designed following the concept of model framework as in Catalysis. This sort of framework can be used as a template to generate code components within an application domain. According to this approach we can develop WFM components that can interoperate within a well‐defined enterprise framework. This paper also presents the process of developing interoperable code components from model frameworks. Copyright © 2002 John Wiley & Sons, Ltd.
Using execution trace data to improve distributed systems
Authors: Moe Johan , Carr David A. 
Published: October 2002

AbstractOne of the most challenging problems facing today's software engineer is to understand and modify distributed systems. One reason is that in actual use systems frequently behave differently than the developer intended. In order to cope with this challenge, we have developed a three‐step method to study the run‐time behavior of a distributed system. First, remote procedure calls are traced using CORBA interceptors. Next, the trace data is parsed to construct RPC call‐return sequences, and summary statistics are generated. Finally, a visualization tool is used to study the statistics and look for anomalous behavior. We have been using this method on a large distributed system (more than 500000 lines of code) with data collected during both system testing and operation at a customer's site. Despite the fact that the distributed system had been in operation for over three years, the method has uncovered system configuration and efficiency problems. Using these discoveries, the system support group has been able to improve product performance and their own product maintenance procedures. Copyright © 2002 John Wiley & Sons, Ltd.
Effect of SA4503 on the electrically evoked release of 3H‐acetylcholine from striatal and hippocampal rat brain slices
Authors: Horan Bryan , Gifford Andrew N. , Matsuno Kiyoshi , Mita Shiro , Ashby Charles R. 
Published: October 2002

AbstractRecent microdialysis data has shown that the systemic administration of the selective σ1 receptor agonist SA4503 increases the extracellular levels of acetylcholine (ACh) in the hippocampus, but not the striatum, of freely moving rats. In the present study, we examined the effect of SA4503 on the electrically evoked release of 3H‐ACh in rat brain slices isolated from the hippocampus and striatum. At 100 and 300 nM concentrations of SA4503, the electrically evoked release of 3H‐ACh was increased in hippocampal but not striatal slices. Concentrations below 100 nM did not alter the electrically evoked release of 3H‐ACh in either brain area. These results tentatively suggest that the increase in extracellular ACh levels observed in the hippocampus after the systemic administration of SA4503 could in part be related to its interaction with σ1 receptors in the hippocampus. Synapse 46:1–3, 2002. © 2002 Wiley‐Liss, Inc.
Teacher communication behavior and its association with students' cognitive and attitudinal outcomes in science in Taiwan
Authors: She Hsiao‐Ching , Fisher Darrell 
Published: October 2002

AbstractIn the study described in this article a questionnaire was employed that can be used to assess students' and teachers' perceptions of science teachers' interpersonal communication behaviors in their classroom learning environments. The Teacher Communication Behavior Questionnaire (TCBQ) has five scales: Challenging, Encouragement and Praise, Non‐Verbal Support, Understanding and Friendly, and Controlling. The TCBQ was used with a large sample of secondary science students in Taiwan, which provided additional validation data for the TCBQ for use in Taiwan and cross‐validation data for its use in English‐speaking countries. Girls perceived their teachers as more understanding and friendly than did boys, and teachers in biological science classrooms exhibited more favorable behavior toward their students than did those in physical science classrooms. Differences were also noted between the perceptions of the students and their teachers. Positive relationships were found between students' perceptions of their teachers' communication behaviors and their attitudes toward science. Students' cognitive achievement scores were higher when students perceived their teacher as using more challenging questions, as giving more nonverbal support, and as being more understanding and friendly. The development of both teacher and student versions of the TCBQ enhances the possibility of the use of the instrument by teachers. © 2002 John Wiley & Sons, Inc. J Res Sci Teach 39: 63–78, 2002
Developing effective intercultural relationships: The importance of communication strategies
Authors: Harvey Michael G. , Griffith David A. 
Published: October 2002

AbstractAs global competition intensifies, it is becoming necessary for organizations to establish strong intercultural

relationships with a culturally diverse set of employees, interorganizational partners as well as customers. In

order to manage these relationships effectively, organizations need a means to understand and improve global

intercultural communications. The complexity of intercultural communications requires management to understand the

nature of domains of global relationships and the level of complexity when attempting to communicate with multiple

partners having unique national and organizational cultures. In this article, a decision process for developing

effective intercultural communication strategies is developed, illustrating the steps necessary for managing a

myriad of intercultural relationships. © 2002 Wiley Periodicals, Inc.
Toxicity assessment of cyanobacterial toxin mixtures
Authors: Wolf Hans Uwe , Frank Christian 
Published: October 2002

AbstractA method is presented for the toxicity assessment of mixtures of cyanobacterial toxins with hepatotoxic, neurotoxic, and carcinogenic effects. The method is based on the derivation of toxicity equivalent factors obtained from toxicological data presented for cyanobacterial toxins in the literature and on the use of toxicity equivalents in analogy with the method used for polychlorinated dibenzo[p]dioxins and dibenzofurans. Because the method easily can include all toxicological data for cyanobacterial toxins at any time, the quality of the toxicity assessment of these toxins can be increased continuously depending on data availability. Generally, all toxicologically relevant cyanobacterial toxins for which data are available should be included in this assessment. The method is considered useful in the toxicity assessment of cyanobacterial toxin mixtures in surface water bodies and in drinking water. When using the total sum of the toxicity equivalents, the approach proposed here seems to lead to a more realistic toxicity assessment of cyanobacterial toxin mixtures than does the worst‐case approach. However, the availability of data about acute and, especially, chronic toxicity must be increased significantly in the future in order to establish toxicologically validated exposure limit values for cyanobacterial toxins, especially those with hepatotoxic, neurotoxic, and carcinogenic effects. © 2002 Wiley Periodicals, Inc. Environ Toxicol 17: 395–399, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/tox.10066
Examination of compound formation at interface of tin–bismuth–silver solder and copper substrate by using electron probe micro analysis
Authors: Tanabe T. , Harada S. 
Published: October 2002

AbstractThe wettability of tin–bismuth–silver solders on copper was studied by using energy‐dispersive x‐ray spectrometry (EDXRS) for elemental analysis. Four kinds of fluxes were used. The wettability of conventional eutectic tin–lead solder was much higher than that of solders based on tin–bismuth systems. The poor wettability of tin–bismuth solders may be caused by the growth of dendritic copper–tin compounds at the copper/solder interface, in contrast to the case of tin–lead solder. The wettability was improved by addition of silver to the solder. In the tin–bismuth–silver system, EDXRS mapping of elements revealed that silver was abnormally concentrated at the copper/solder interface even in the initial stage of their contact. When using FR‐type fluxes, the solder exhibited maximum wettability in the range from 1–4 mass% Ag addition. The layer thickness of the Cu–Sn compound formed on Cu was smallest with a 2% Ag addition. This may correspond to the improvement of the solder wettability. Copyright © 2002 John Wiley & Sons, Ltd.