bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critical analysis of continuum electrostatics: The screened Coulomb potential–implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins
Authors: Hassan Sergio A. , Mehler Ernest L. 
Published: October 2004

AbstractAn analysis of the screened Coulomb potential–implicit solvent model (SCP–ISM) is presented showing that general equations for both the electrostatic and solvation free energy can be derived in a continuum approach, using statistical averaging of the polarization field created by the solvent around the molecule. The derivation clearly shows how the concept of boundary, usually found in macroscopic approaches, is eliminated when the continuum model is obtained from a microscopic treatment using appropriate averaging techniques. The model is used to study the alanine dipeptide in aqueous solution, as well as the discrimination of native protein structures from misfolded conformations. For the alanine dipeptide the free energy surface in the ϕ–ψ space is calculated and compared with recently reported results of a detailed molecular dynamics simulation using an explicit representation of the solvent, and with other available data. The study showed that the results obtained using the SCP–ISM are comparable to those of the explicit water calculation and compares favorably to the FDPB approach. Both transition states and energy minima show a high correlation (r > 0.98) with the results obtained in the explicit water analysis. The study of the misfolded structures of proteins comprised the analysis of three standard decoy sets, namely, the EMBL, Park and Levitt, and Baker's CASP3 sets. In all cases the SCP–ISM discriminated well the native structures of the proteins, and the best‐predicted structures were always near‐native (cRMSD ∼2 Å). Proteins 2002;47:45–61. © 2002 Wiley‐Liss, Inc.
Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation
Authors: Falconi M. , Parrilli L. , Battistoni A. , Desideri A. 
Published: October 2004

AbstractLimited proteolysis by trypsin of monomeric Cu,Zn superoxide dismutase from Escherichia coli induces a specific cleavage of the polypeptide chain at the level of Lys60 located in the S–S subloop of loop 6,5 where, when compared to the eukaryotic enzyme, a seven‐residues insertion, completely exposed to the solvent, is observed. This result suggests that this subloop is disordered and flexible, thus enabling binding and adaptation to the active site of the proteolytic enzyme. Indeed, molecular dynamics simulation indicates that the S–S subloop undergoes high fluctuations and that its high flexibility coupled to an high solvent accessibility can explain the specific bond selection of the protease. As a matter of fact, of the possible 14 solvent accessible proteolytic sites only the Lys60 flexible site is cleaved. High flexibility and solvent exposure are confirmed by the short water residence time for the residues corresponding to the cleavage site evaluated by molecular dynamics simulation. These experiments demonstrate that molecular dynamics simulation and limited proteolysis are complementary and unambiguous tools to identify flexible sites in proteins. Proteins 2002;47:513–520. © 2002 Wiley‐Liss, Inc.
Computational studies on density function theory for the bimolecular metathesis reaction CH3+HCl⇔︁CH4+Cl
Authors: Zhou Zhengyu , Chen Guang , Zhou Xingmin , Fu Hui 
Published: October 2004

AbstractDensity function theory has been applied to alkyl radical reaction to get helpful data for its geometric parameters, energy, and vibrational frequency compared with results obtained by ab initio methods and experimental values. The geometry optimization of the transition state, the precursor complex and the successor complex were performed at the 6‐311G* basis set level. The transition state of the CH4Cl system of the reaction computed was in agreement with the prediction of Benson. From analysis of the vibration frequency and the net charge on the atom of the precursor complex, transition state, successor complex and the isolated state, the reaction mechanism was derived which we complicated with the bond‐rupture electron‐transfer theory. The atom H in molecule HCl attacks the atom C, forming a transition state via the precursor complex and the electron transfer happens in the precursor complex. The reaction rate of the electron transfer determines the rate of the whole reaction to a certain extent, and active energy, electronic coupling matrix element, and reorganization energy were obtained. © 2001 Wiley Periodicals, Inc. Int J Quantum Chem, 2001
High‐spin silicon fullerene Si60 and its oligomers
Authors: Sheka Elena F. , Nikitina Ekaterina A. , Zayets Valentin A. , Ginzburg Ilya Ya. 
Published: October 2004

AbstractHigh‐spin states of the Si60 fullerene and its oligomers are considered semiempirically by using sequential and parallel implementations of the AM1 codes. The states are energetically favorable and nearly degenerated over triplet, quintet, and septet spins. All atoms of the Si60 fullerene are in sp3‐configuration, which is supported by atomic spin density in addition to electron density, the latter to be responsible for the formation of chemical bonds. Spotted distribution of spin density over atoms provides molecular magnetism of the molecule. A similar picture is disclosed for oligomers {Si60}n with n up to 8, which according to computational results should be magnetic with a fractal‐like distribution of spin density over atoms. Opposite the latter, composites Si60C60 and Si60H60 behave conventionally and are nonmagnetic. A way of the Si60 fullerene synthesizing is suggested via the above composite product as intermediates. The considered oligomers are proposed as a model of silicon nanofibers observed recently. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Reactivity of molecular oxygen on the surface of ionic crystals
Authors: Mikheikin I. D. , Vorontsova I. K. , Abronin I. A. 
Published: October 2004

AbstractA possibility of multiplicity change for ground‐state molecular oxygen adsorbed on the surface of regular and doped broad‐gap ionic crystals was considered in the framework of cluster approximation by using SCF MO LCAO quantum chemical methods [semiempirical INDO approximation and ab initio calculation with the 6‐311G** basis set taking into account the correlation effects on the level of second‐order Meller–Plesset perturbation theory (MP2)]. The formation energetics of cyclic products of addition reactions of dioxygen in different multiplet states to furan and cis‐butadiene in the gas phase and on the surface of ionic crystals was considered. (These reactions are typical for the O2 singlet state in the gas phase.) It is shown that the presence of sites with high effective charge on the crystal surface can result in a situation not requiring, as in the gas phase, multiplicity change in the transition of a system from an initial to the final state, which can significantly affect the kinetic parameters of the reactions. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Investigation of structure of Fe3+ magnetic center in polyparaphenylene
Authors: Vasyukov V. N. , Shapovalov V. A. , Dyakonov V. P. , Dmitruk A. F. , Aksimentjeva E. I. , Szymczak H. , Piechota S. 
Published: October 2004

AbstractIn the temperature range between 4.2 and 300 K, the EPR spectrum of the impurity Fe3+ ion in the organic polyparaphenylene has been investigated. An effect developed as an unusual temperature change of Fe3+ EPR spectrum has been revealed. The EPR spectrum of powder sample consists of two resonance lines. Line 1 with the effective g‐value equal to g1 = 4.21 ± 0.05 is of the maximum intensity at T = 4.2 K. With temperature increase, the intensity of line 1 decreases until vanishing. Line 2 is observed over the whole temperature range. For T = 300 K, the g‐value of line 2 is g2 = 2.00 ± 0.09. To study the structure of magnetic ion molecular environment and define nonequivalent positions of the magnetic ion in polyparaphenylene, a calculation was done of the energy of Fe3+ magnetic ion for various possible molecular environments. It is shown that in polyparaphenylene for the Fe3+ magnetic ion there are two different stationary molecular environments. The obtained model of magnetic ion molecular environment was used to explain the temperature dependence of the EPR spectrum. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
A GUI software development system for digital AV applications
Authors: Haruna Shuusuke , Sanada Norio , Kinoh Hisayuki , Sumiya Kazutoshi , Taki Kazuo 
Published: October 2004

AbstractThe scale of software on digital AV appliances that handle large‐volume multichannel digital data has been increased by the GUIs (graphical user interfaces) loaded on them in recent years. In addition, the GUIs of AV appliances use remote controls having cursor keys. Focus management must be performed by these to point to the object of operation, in contrast to the mouse, which is capable of pointing on the entire screen. Since focus management changes with changes in the specifications of GUIs, such as screen layouts and the like, software may not be reusable. In this paper, a development system that attempts to improve the productivity of GUI software requiring focus management is discussed from the points of view of (1) a software design model based on an object‐oriented MVC model, (2) an execution model with good efficiency corresponding to the design model, (3) development tools performing synthesis of GUI software and automatic generation of focus management procedures, and (4) applications and evaluations of the system. In an example of the application of the system, software productivity with a GUI specification change was improved by a factor of three. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(7): 99–107, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10018
Equivalence of real‐time DPDAs and discrete extended simple recurrent networks with some restrictions
Authors: Moriya Junnosuke , Nishino Tetsuro 
Published: October 2004

AbstractTo model human natural language processing using computation theory, Elman proposed a simple recurrent network. A simple recurrent network is a recurrent neural network with restrictions added to the connections between gates. When the range of the function for computing each gate of a simple recurrent network is a finite set (this is called a discrete simple recurrent network), its computational capability is known to be equivalent to that of a finite automaton with output. This paper introduces a modification of a discrete simple recurrent network so that it has a computational capability equivalent to that of a real‐time deterministic pushdown automaton (real‐time DPDA). In other words, the discrete simple recurrent network is extended as follows. (1) It contains a number of gates equal to a constant multiple of the input length, and (2) those gates can be used to simulate a stack with a depth of at most the input length. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(7): 55–62, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10275
Learning and inference in hierarchical models with singularities
Authors: Amari Shun‐ichi , Ozeki Tomoko , Park Hyeyoung 
Published: October 2004

AbstractWhen we infer the underlying rule which generates a large amount of data, we assume a family of hierarchical statistical models and estimate an appropriate model and its parameters. In this case, the parameter space of the model usually includes singularities, and interesting phenomena, different from those appearing in conventional inference theory, are observed. In this paper, we review the studies of singular models in learning and inference which are being extensively developed in Japan, and elucidate the mechanisms of strange behavior by using simple models. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(7): 34–42, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10353
Coupled Markov random field models with phases as line field and region field
Authors: Tanaka Kazuyuki , Furusato Daiki , Horiguchi Tsuyoshi 
Published: October 2004

AbstractWe investigate a boundary‐based and a region‐based coupled Markov random field model, both of which are useful in image restorations of gray‐level images. In the conventional boundary‐based and the conventional region‐based coupled Markov random field models, both a line field and a region field take only two discrete states, 0 and 1. In the boundary‐based coupled random field model, existence and nonexistence of the edge at each nearest‐neighbor pair of pixels are denoted by 1 and 0, respectively. In the region‐based coupled random field model, some different regions at each pixel are labeled by discrete numbers. We propose a boundary‐based coupled Markov random field model with continuous line field and a region‐based coupled Markov random field model with continuous segmentation field from a standpoint of a plane rotator model in statistical mechanics. The iterative algorithms for image restoration are constructed by using a mean‐field approximation. We investigate how the proposed models produce a better quality of restored images. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(7): 24–33, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10364
Potential genotoxicity of wastewater‐contaminated pore waters with comparison to sediment toxicity and macrobenthic community composition*
Authors: Lewis Michael A. , Daniels Carol B. , Moore James C. , Chen Thomas 
Published: October 2004

AbstractThe objectives of this survey were to determine the genotoxic potential of sediment pore waters above and below 10 wastewater outfalls and to compare the results to sediment chemical quality guidelines, acute toxicity, and macrobenthic community composition. The focus of the study was on genotoxicity since its occurrence in environmental media below wastewater discharges in the Gulf of Mexico region has not been reported in the scientific literature. Pore waters from 43 sediment samples were assayed using a microbial mutagenicity assay before and after activation with a rat liver microsome mix (S‐9). A combination of either direct or activated responses was observed for 40% of the pore waters. Direct, activated, and both direct and activated responses were observed in 5, 26, and 9% of the total samples, respectively. Mutagenic effects were observed below 7 of the 10 outfall areas and in 4 of 6 control areas associated with 6 outfalls. The lowest pore water concentrations causing an activated mutagenic response were statistically similar above and below the outfalls. Mutagenicity occurred more frequently than acute toxicity to estuarine and freshwater invertebrates and there was no consistent relationship between its occurrence and the exceedance of sediment chemical quality guidelines. In contrast, there was some indication that mutagenic activity paralleled low benthic community diversity. © 2002 by Wiley Periodicals, Inc. Environ Toxicol 17: 63–73, 2002
A systematic review of the ultrasound estimation of fetal weight
Authors: Dudley N. J. 
Published: October 2004

AbstractObjectivesThe range and use of ultrasound fetal measurements have gradually been extended. Measurements have been combined to estimate fetal weight by mathematically based non‐linear regression analysis or physically based volumetric methods. Fetal weight estimation is inaccurate, with poor sensitivity for prediction of fetal compromise. Several authors have shown the unacceptable level of intra‐ and interobserver variability in fetal measurement and the impact of errors on growth assessment. The aims of this study were to review the available methods and possible sources of inaccuracy.MethodsFour databases were searched for studies comparing ultrasound estimated fetal weight (EFW) with birth weight. Studies meeting the inclusion criteria evaluated 11 different methods. Errors were graphically summarized.ResultsNo consistently superior method has emerged. Volumetric methods provide some theoretical advantages. Random errors are large and must be reduced if clinical errors are to be avoided.ConclusionsThe accuracy of EFW is compromised by large intra‐ and interobserver variability. Efforts must be made to minimize this variability if EFW is to be clinically useful. This may be achieved through averaging of multiple measurements, improvements in image quality, uniform calibration of equipment, careful design and refinement of measurement methods, acknowledgment that there is a long learning curve, and regular audit of measurement quality. Further work to improve the universal validity and accuracy of fetal weight estimation formulae is also required. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
The Changing Demographics of Head and Neck Squamous Cell Carcinoma in the United States
Authors: Sikora Andrew G. , Toniolo Paolo , DeLacure Mark D. 
Published: October 2004

AbstractObjectives/Hypothesis: Head and neck squamous cell carcinoma (HNSCCA) has declined in the United States since the late 1970s. During this time, substantial immigration from other countries has occurred, and the average lifespan has increased. We tested the hypothesis that these trends have altered the HNSCCA patient population.Study Design: Retrospective analysis was made of population‐based data from the SEER database, a national registry capturing roughly 10% of all U.S. cancer diagnoses.Methods: We examined all unique diagnoses of HNSCCA in the database from 1976 to 1999 and determined the breakdown of cases by age, sex, and race.Results: The absolute number of new HNSCCA diagnoses per year declined overall by 5% during the time period of the study, whereas new diagnoses in patients older than 74 years of age increased by more than 20%. The rate of HNSCCA per 100,000 person‐years in elderly women did not change, and the rate in elderly men decreased, indicating that the observed increase in cases is explained by a growing population of elderly persons at risk. An increase in the absolute number of cases, but not the incidence rate, was also seen among persons younger than 50 years of age. Although both the absolute number of new cases and the incidence rates of HNSCCA in white male patients declined substantially, the percentage of HNSCCA patients classified as minorities increased from 14.5% to more than 20% of all cases. During the time period of the study, the overall number of HNSCCA cases in nonwhite and Hispanic patients increased by 36%.Conclusion: Increasing numbers of elderly and minority patients with HNSCCA are likely to alter patterns of disease and utilization of health care resources.
Endolymphatic Duct Violation During Retrosigmoid Dissection of the Internal Auditory Canal: A Human Temporal Bone Radiographic Study
Authors: Sulman Cecille G. , Vecchiotti Mark A. , Semaan Maroun T. , Lewin Jonathan S. , Megerian Cliff A. 
Published: October 2004

AbstractObjective/Hypothesis: Successful hearing preservation after acoustic neuroma resection is sometimes complicated by delayed hearing deterioration. The goal of this study was to investigate the hypothesis that internal auditory canal (IAC) drilling during retrosigmoid acoustic neuroma removal may result in endolymphatic duct (ELD) injury, a potential cause of delayed hearing loss (HL) after hearing preservation surgery.Study Design: Temporal bone anatomic and radiographic study and literature review.Methods: Twenty‐one human temporal bones were analyzed with high‐resolution multislice computed tomography (HRMCT) and subjected to standard retrosigmoid IAC dissection with labyrinthine preservation and follow‐up HRMCT for analyses of the ELD. A MEDLINE search was performed of studies documenting long‐term hearing preservation outcomes after retrosigmoid dissection.Results: Five of 21 (24%) bones were found to have violation of the ELD despite preservation of labyrinthine structures and the endolymphatic sac. These results correlate with the mean incidence of long‐term hearing decline (26.6%). Reviews of human and animal studies indicate that injury to the ELD may create endolymphatic hydrops.Conclusions: The ELD is vulnerable to injury during IAC dissection even if labyrinthine structures at the lateral aspect of the IAC are preserved. These findings may be helpful in explaining and potentially preventing some cases of long‐term hearing deterioration that may be a result of endolymphatic hydrops after ELD injury during acoustic tumor removal. Careful preoperative review of imaging studies using HRMCT may prove useful before retrosigmoid dissection.
Speech Intelligibility and Quality of Life in Head and Neck Cancer Survivors
Authors: Meyer Tanya K. , Kuhn Joan C. , Campbell Bruce H. , Marbella Anne M. , Myers Katherine B. , Layde Peter M. 
Published: October 2004

AbstractObjective: Poor speech intelligibility adversely affects quality of life self‐assessment in long term survivors of head and neck cancer treatment.Study Design: Observational case series including both objective clinical speech testing and subjective quality of life questionnaire administration.Methods: Five‐year head and neck cancer survivors were recruited to study the association between speech intelligibility and quality of life. Survivors were analyzed as an entire group, and also subdivided into laryngectomees and non‐laryngectomees. Objective testing included sentence and word intelligibility. Subjective testing included quality of life questionnaires (UWQOL, FACT, FACT‐head and neck, and PSS‐HN) and a locally prepared “cancer concern” question. Associations were sought between intelligibility, quality of life and demographics.Results: Sixty‐two survivors underwent testing. Lower sentence intelligibility and word intelligibility scores were associated with diminished self‐perceived UWQOL Speech (P = .0001 and P = .0001, respectively) and PSS‐HN Understandability of Speech (P = .009 and P = .005). Decreased word intelligibility was additionally associated with decreased UWQOL Chewing (P = .003), UWQOL Swallowing (P = .02), UWQOL Recreation (P = .05), PSS‐HN Willingness to Eat in Public (P = .03), and PSS‐HN Normalcy of Diet (P = .0001). The associations continued even after patients who had undergone laryngectomy were excluded.Conclusions: Long‐term survivors of head and neck cancer continue to have both objective and subjective deficits in speech parameters five years after treatment. Objective deficits are associated with subjective concerns about speech, eating, and recreation. Understanding how communication deficits affect quality of life in long‐term head and neck cancer survivors may allow more effective therapies to modulate these concerns in the recovery period.