bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation model of nearwork‐induced transient myopia
Authors: Hung George K. , Ciuffreda Kenneth J. 
Published: July 2002

SummaryA nearwork model was developed to determine whether variation in accommodative adaptation gain, KA, can account for the differences in the dynamic decay timecourse following near work in hyperopes (HYP), emmetropes (EMM), early‐onset myopes (EOM), and late‐onset myopes (LOM). The model incorporated a proximal component into a previously‐developed adaptation model of accommodation and vergence. It was used to simulate the nearwork‐induced transient myopia (NITM) response following 10 min of congruent binocular near viewing (5 D, 5 MA). The accommodative adaptation gain, KA, value was varied from 1.0 to 6.0 in increments of 0.5. For the hyperopes, an additional constraint was imposed wherein the accommodative response was biased on the under‐accommodated side of the deadspace operator (i.e., depth‐of‐focus). In addition, the effect of prolonged nearwork was simulated by alternating between 1 hr of congruent near viewing (3 D, 3 MA) and 5 min of congruent far viewing (0.25 D, 0.25 MA) over a 160 hr period representing one work‐month with 40 hours of nearwork per week. The steady‐state rms value of the accommodative error was measured as a function of KA. It was found that the NITM timecourses for HYP, EMM, EOM, and LOM could be simulated accurately using KA values of 2.0, 2.5, 4.0 and 5.5, respectively. The long‐term final steady‐state rms of the accommodative error was found to increase from 0.182 D to 0.188 D as KA increased from 1 to 6. This indicated a small and progressive increase in residual accommodative error for higher KA values, which was associated with EOM and LOM. Thus, NITM for the different refractive groups could be quantified by the accommodative adaptation gain element, with KA for the HYP, EMM, and EOM and LOM groups having lower, intermediate, and higher values, respectively. The larger rms for higher KA values suggests that a myopic individual may have a predisposition to exhibit a slightly larger long‐term accommodative error, which may stimulate axial elongation and in turn promote the progression of axial myopia.
State-specific unimolecular reaction dynamics of HFCO. I. Dissociation rates
Authors: Choi Young S. , Moore C. Bradley 
Published: July 2002

Rovibrationally resolved unimolecular reaction rates of highly vibrationally excited HFCO (S0) are measured and found to be strongly state specific in the energy range of 14 500 cm−1–23 000 cm−1. HFCO molecules are excited to single rovibrational levels in the tunneling region by stimulated emission pumping (SEP) and the dissociation rate of each level is measured by monitoring the temporal evolution of its population by laser-induced fluorescence. The dissociation rates increase by a factor of 10 to 100 or more for small increases in rotational quantum number from J=0 up to J=4 and Ka=2. The dependence on Ka is the strongest. At higher energies, where dissociation lifetimes are shorter than the laser pulse duration, dissociation rates are estimated from the linewidths of well-resolved transition lines measured by high-resolution SEP spectroscopy. In this energy region, dissociation rates are also dependent upon rotational state but much less strongly than in the tunneling region. Vibrational mode specificity in the dissociation rates is observed. For states with approximately the same total energy those with higher excitation in the out-of-plane bending mode (ν6) dissociate more slowly than others. For rotationless levels in the tunneling region, the A′ states decay much more rapidly than the A″ states indicating symmetry-induced mode specificity.
The dissociation rates in HFCO almost surely exhibit mode specificity because the ν6 mode is weakly coupled to the reaction coordinate. The enhancement of this coupling by Coriolis forces appears to produce the unprecedentedly large rotational level dependence of the rates. However, the spectroscopically observed coupling of ν6 to the background of vibrationally mixed levels is not significantly increased by rotation. Thus states with nearly all of the excitation energy in the reaction coordinate appear not to be strongly mixed into the background states. The large effect of rotation on the rates thus seems to result from Coriolis coupling of extreme motion in the reaction coordinate to the background levels or directly to ν6. By applying the Rice–Ramsperger–Kassel–Marcus theory to the measured dissociation rates for high rotational states, the barrier height for the molecular dissociation of HFCO to HF+CO is estimated to be 49±4 kcal/mole.
Applications of multireference perturbation theory to potential energy surfaces by optimal partitioning of H: Intruder states avoidance and convergence enhancement
Authors: Finley James P. , Chaudhuri Rajat K. , Freed Karl F. 
Published: July 2002

The minimum basis set hydrogen rectangular system (HRS), consisting of four hydrogen atoms arranged in a rectangle, is examined using a variety of partitionings of the Hamiltonian H for high order single and double reference perturbation computations. The potential energy surface is mapped out over a range of geometries in which the length L of one side of the rectangle is varied. Several criteria are derived governing the necessary conditions for perturbative convergence of two-state systems, and these criteria are useful in explaining the behavior of the HRS for the range of geometries and partitioning methods investigated. The divergence caused by intruder states, observed by Zarrabian and Paldus [Int. J Quantum Chem. 38, 761 (1990)] for the nondegenerate, double reference space perturbation expansions at L=3.0 a.u. with traditional partitioning methods, is shown to correspond to avoided crossings with negative real values of the perturbation parameter—backdoor intruder states. These intruder state induced divergences result from too small zeroth order energy differences between the high lying reference space state and an orthogonal space intruder state whose identity depends on the partitioning method. Forcing the valence orbitals to be degenerate enlarges these zeroth order energy differences and, thus, yields a convergent perturbative expansion for L=3.0 a.u.
The convergent or divergent behavior of all the partitioning method computations and the locations of their avoided crossings are accurately predicted by using two-state models composed of the high lying reference space state and the intruder state. A partitioning method is introduced in which the zeroth order state energies are selected to optimize the convergence in low orders of the perturbation expansion. This optimization method yields perturbative convergence which is both rapid and free of intruder state for geometries between L=2.0 and 3.0 a.u. The divergent behavior for various partitioning methods at L=5.0 a.u., also observed by Zarrabian and Paldus, is caused by one or more orthogonal space states and the high lying reference space state that are strongly coupled and have close expectation values of H. The two-state model illustrates why no partitioning choice with a double reference space can yield a satisfactory rate of perturbative convergence for L=5.0. Therefore, the entire potential energy surface is treated using more than one reference space: a double reference space for L≤3.0 a.u. and a single reference space for L≳3.0 a.u. The entire potential surface of interest, which is generated with the optimized partitioning method and the two different reference spaces, is very accurate by third order, with eigenvalues for all geometries considered differing from the FCI by no more than 1 kcal/mol.
Imaging of Primitive Neuroectodermal Tumor (PNET) by Technetium‐99m Tetrofosmin
Authors: Karanikas Georgios , Köstler Wolfgang , Becherer Alexander , Dudczak Robert , Krainer Michael , Kletter Kurt 
Published: July 2002

Purpose. Tc‐99m tetrofosmin launched for myocardial studies has recently also shown a good detectability for several tumors.
Data on PNET imaging by Tc‐99m tetrofosmin are not yet available.Patient and method. In the case of a 21‐year‐old man suffering from pelvis PNET, Tc‐99m tetrofosmin scintigraphy was
performed additionally to CT and MRI.Results. The gluteal and iliac tumor masses were visualized by Tc‐99m tetrofosmin according to the CT and MRI results.Discussion. Imaging with Tc‐99m tetrofosmin could provide additional information to the available conventional radiological
imaging modalities for diagnosis of PNET, and could be a useful tool for the restaging of the primary tumor.
Role of ERK and p38 Mitogen‐Activated Protein Kinase Cascades in Gastric Mucosal Inflammatory Responses to Helicobacter pylori Lipopolysaccharide
Authors: Slomiany Bronislaw L. , Slomiany Amalia 
Published: July 2002

AbstractThe animal model of H. pylori lipopolysaccharide (LPS)‐induced gastritis was used to study the role of extracellular signal‐regulated kinase (ERK) and p38 mitogen‐activated protein kinase (MAPK) in the mucosal release of tumor necrosis factor‐ α (TNF‐ α) and endothelin‐1 (ET‐1) in response to H. pylori infection. Rats, pre‐treated with specific inhibitors of p38 and ERK pathways, SB203580 and PD98059, were submitted to intragastric application of H. pylori LPS and maintained on the daily regimen of the inhibitors for 4 days. In the absence of inhibitors, the LPS elicited a pattern of mucosal inflammatory responses resembling that of acute gastritis, and reflected in a massive increase in the mucosal level of ET‐1 and TNF‐ α. Administration of SB203580 led to a 63.4% reduction in the extent of inflammatory involvement, the level of ET‐1 fell by a 42% and TNF‐ α declined by a 52.3%, whereas PD98059 elicited a 21.2% reduction in the extent of inflammatory involvement and a 22.7% decrease in TNF‐ α, but had no effect on the LPS‐induced increase in ET‐1. A combination of both inhibitors, while exerting additive effect on TNF‐ α, produced no additional reduction in ET‐1 and the extent of inflammatory involvement achieved with SB203580 alone. The findings suggest that the p38 MAPK signaling pathway plays a key role in the mediation of gastric mucosal inflammatory reaction to H. pylori infection.
A new publishing paradigm: STM articles as part of the semantic web
Authors: Rzepa Henry S. , Murray‐Rust Peter 
Published: July 2002

ABSTRACTAn argument is presented for replacing the traditional published scientific technical or medical article, where heavy reliance is placed on human perception of a printed or a printable medium, by a more data‐centric model with well‐defined structures expressed using XML languages. Such articles can be regarded as self‐defining or ‘intelligent’: they can be scaled down to fine‐level details such as, for example, atoms in molecules, up into journals or higher‐order collections, and can be used by software agents as well as humans. Our vision is that this higher‐order concept, often referred to as the semantic web, would lay the foundation for the creation of an open and global knowledge base.
Variations on conservation laws for the wave equation
Authors: Morawetz Cathleen 
Published: July 2002

The first part of this paper, presented as an Emmy Noether lecture in connection with the ICM in Berlin in August 1998, gives some examples of using Noether’s theorem for conservation laws for Tricomi-like equations and for the wave equation. It is also shown that equations which are semilinear variations of the wave equation can very often be handled similarly. The type of estimate obtained can even be used to get otherwise unobtainable local estimates for regularity. The fourth part is an introduction to the relation of black holes to the wave equation mainly showing the results of D. Christodoulou. His results use much more difficult estimates not corresponding at all to those in the first part of the paper.
Comparative accuracy of methods for protein sequence similarity search.
Authors: Agarwal P , States D J 
Published: July 2002

Abstract
MOTIVATION: Searching a protein sequence database for homologs is a powerful tool for discovering the structure and function of a sequence. Two new methods for searching sequence databases have recently been described: Probabilistic Smith-Waterman (PSW), which is based on Hidden Markov models for a single sequence using a standard scoring matrix, and a new version of BLAST (WU-BLAST2), which uses Sum statistics for gapped alignments. RESULTS: This paper compares and contrasts the effectiveness of these methods with three older methods (Smith-Waterman: SSEARCH, FASTA and BLASTP). The analysis indicates that the new methods are useful, and often offer improved accuracy. These tools are compared using a curated (by Bill Pearson) version of the annotated portion of PIR 39. Three different statistical criteria are utilized: equivalence number, minimum errors and the receiver operating characteristic. For complete-length protein query sequences from large families, PSW's accuracy is superior to that of the other methods, but its accuracy is poor when used with partial-length query sequences. False negatives are twice as common as false positives irrespective of the search methods if a family-specific threshold score that minimizes the total number of errors (i.e. the most favorable threshold score possible) is used. Thus, sensitivity, not selectivity, is the major problem. Among the analyzed methods using default parameters, the best accuracy was obtained from SSEARCH and PSW for complete-length proteins, and the two BLAST programs, plus SSEARCH, for partial-length proteins.
Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment.
Authors: Gracy J , Argos P 
Published: July 2002

Abstract
MOTIVATION: Genome sequencing projects require the periodic application of analysis tools that can classify and multiply align related protein sequence domains. Full automation of this task requires an efficient integration of similarity and alignment techniques. RESULTS: We have developed a fully automated process that classifies entire protein sequence databases, resulting in alignment of the homologous sequences. The successive steps of the procedure are based on compositional and local sequence similarity searches followed by multiple sequence alignments. Global similarities are detected from the pairwise comparison of amino acid and dipeptide compositions of each protein. After the elimination of all but one sequence from each detected cluster of closely related proteins, the remaining sequences are compiled in a suffix tree which is self-compared to detect local sequence similarities. Sets of proteins which share similar sequence segments are then weighted according to their closeness and multiply aligned using a fast hierarchical dynamic programming algorithm. Computational strategies were devised to minimize computer processing time and memory space requirements. The accuracy of the sequence classifications has been evaluated for 12 462 primary structures distributed over 341 known families. The percentage of sequences with missed or incorrect family assignments was 6.8% on the test set. This low error level is only twice that of the manually constructed PROSITE database ( 3.4% ) and is substantially better than that found for the automatically built PRODOM database ( 34.9% ). AVAILABILITY: The resulting database, called DOMO, is available through database search routine SRS at Infobiogen (http://www.infobiogen.fr/srs5/), EBI (http://srs.ebi.ac.uk:5000/) and EMBL (http://www.embl-heidelberg.de/srs5/) World Wide Web sites. CONTACT: gracy@infobiogen.fr
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
Authors: Yada T , Totoki Y , Ishikawa M , Asai K , Nakai K 
Published: July 2002

Abstract
MOTIVATION: Automatic extraction of motifs that occur frequently on a set of unaligned DNA sequences is useful for predicting the binding sites of unknown transcription factors. Several programs for this purpose have been released. However, in our opinion, they are not practical enough to be applied to a large number of upstream sequences. RESULTS: We propose a new program called YEBIS (Yet another Environment for the analysis of BIopolymer Sequences) which is capable of extracting a set of motifs, without any a priori knowledge, from a number of functionally related DNA sequences. Using the hidden Markov model, these motifs are represented in a more general form than other conventional methods, such as the weight matrix method. When applied to several sets of benchmark data, it was found that YEBIS had comparable capability to the existing methods, but was much faster. Moreover, it could extract all known motifs from the LTR sequences (long terminal repeat sequences) in a single run. Finally, it could be successfully applied to approximately 400 human promoter sequences and some of the extracted motifs turned out to be known cis-elements. Therefore, YEBIS could be a practical tool for exploring the upstream sequences of genomic ORFs, some of which are regulated in a similar fashion. AVAILABILITY: YEBIS will be distributed to academic users free of charge. All requests should be sent to the address below. CONTACT: E-MAIL: yada@tokyo.jst.go.jp
Gene recognition by combination of several gene-finding programs.
Authors: Murakami K , Takagi T 
Published: July 2002

Abstract
MOTIVATION: A number of programs have been developed to predict the eukaryotic gene structures in DNA sequences. However, gene finding is still a challenging problem. RESULTS: We have explored the effectiveness when the results of several gene-finding programs were re-analyzed and combined. We studied several methods with four programs (FEXH, GeneParser3, GEN-SCAN and GRAIL2). By HIGHEST-policy combination method or BOUNDARY method, approximate correlation (AC) improved by 3-5% in comparison with the best single gene-finding program. From another viewpoint, OR-based combination of the four programs is the most reliable to know whether a candidate exon overlaps with the real exon or not, although it is less sensitive than GENSCAN for exon-intron boundaries. Our methods can easily be extended to combine other programs. AVAILABILITY: We have developed a server program (Shirokane System) and a client program (GeneScope) to use the methods. GeneScope is available through a WWW site (http://gf.genome.ad.jp/). CONTACT: (katsu,takagi)@ims.u-tokyo.ac.jp
WebPHYLIP: a web interface to PHYLIP
Authors: Lim Allison , Zhang Louxin 
Published: July 2002

Abstract
Summary: A web interface to PHYLIP (version 3.57 C) is implemented using CGI/Perl programming. It enables users to do phylogenetic analysis through the Internet.
Availability: WebPHYLIP is available at http://sdmc.krdl.org.sg:8080/~lxzhang/phylip.
Contact: lxzhang@krdl.org.sg
Modeling and predicting transcriptional units of
Escherichia coligenes using hidden Markov models
Authors: Yada Tetsushi , Nakao Mitsuteru , Totoki Yasushi , Nakai Kenta 
Published: July 2002

Abstract
Motivation: The hidden Markov model (HMM) is a valuable technique for gene-finding, especially because its flexibility enables the inclusion of various sequence features. Recent programs for bacterial gene-finding include the information of ribosomal binding site (RBS) to improve the recognition accuracy of the start codon, using this feature. We report here our attempt to extend the model into the total transcriptional unit, enabling the prediction of operon structures.
Results: First, we improved the prediction accuracy of coding sequences (CDSs) by employing the models of ‘typical’, ‘atypical’ and ‘negative (false-positive)’ classes as well as the models of RBS and its downstream spacer. The sensitivity of exactly predicting the 204 experimentally confirmed CDSs reached 90.2% in an objective test. Based on the prediction result of CDSs, the positions of the promoters and terminators were predicted. Our model could exactly recognize 60% of 390 known transcriptional units. Thus, the accuracy and significance of this prediction problem is far from trivial. We would like to propose this problem as an open theme in bioinformatics because the ongoing or planned post-sequencing projects will produce much data for future improvements.
Availability: The table of predicted transcriptional units of Escherichia coli will be distributed upon request.
Contact: knakai@ims.u-tokyo.ac.jp
A novel method for automatic functional annotation of proteins.
Authors: Fleischmann W , M√∂ller S , Gateau A , Apweiler R 
Published: July 2002

Abstract
MOTIVATION: To cope with the increasing amount of sequence data, reliable automatic annotation tools are required. The TrEMBL database contains together with SWISS-PROT nearly all publicly available protein sequences, but in contrast to SWISS-PROT only limited functional annotation. To improve this situation, we had to develop a method of automatic annotation that produces highly reliable functional prediction using the language and the syntax of SWISS-PROT. RESULTS: An algorithm was developed and successfully used for the automatic annotation of a testset of unknown proteins. The predicted information included description, function, catalytic activity, cofactors, pathway, subcellular location, quaternary structure, similarity to other protein, active sites, and keywords. The algorithm showed a low coverage (10%), but a high specificity and reliability. AVAILABILITY: The results can be obtained by anonymous ftp from ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb. The source code is available on request from the authors.
MAD: a suite of tools for microarray data management and
processing
Authors: Liao Birong , Hale Walker , Epstein Charles B. , Butow Ronald A. , Garner Harold R. 
Published: July 2002

Abstract
Summary: Microarray data management and processing (MAD) is a set of Windows integrated software for microarray analysis. It consists of a relational database for data storage with many user-interfaces for data manipulation, several text file parsers and Microsoft Excel macros for automation of data processing, and a generator to produce text files that are ready for cluster analysis.
Availability: Executable is available free of charge on http://pompous.swmed.edu. The source code is also available upon request.
Contact: garner@swmed.edu
Circles: automating the comparative analysis of RNA secondary

structure
Authors: Page Roderic D.M. 
Published: July 2002

Abstract
Summary: Circles is a program for inferring RNA secondary structure using maximum weight matching. The program can read in an alignment in FASTA, ClustalW, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in various file formats.
Availability: The program is available at no cost from http://taxonomy.zoology.gla.ac.uk/rod/circles/ and requires Windows 95/98/NT.
Contact: r.page@bio.gla.ac.uk
model.it : building three dimensional DNA models from
sequence data
Authors: Vlahovic̆ek Kristian , Pongor Sándor 
Published: July 2002

Abstract
Summary: A WWW server is described for creating 3D models of canonical or bent DNA starting from sequence data. Predicted DNA trajectory is first computed based on a choice of di- and tri-nucleotide models (M.G.Munteanu et al. , Trends Biochem. Sci.23, 341–347, 1998); an atomic model is then constructed and optionally energy-minimized with constrained molecular dynamics. The data are presented as a standard PDB file, directly viewable on the user’s PC using any molecule manipulation program.
Availability: The model.it server is freely available at http://www.icgeb.trieste.it/dna/
Contact: kristian@icgeb.trieste.it; pongor@icgeb.trieste.it
Supplementary information: A series of help files is available at the above address.