bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher analytic derivatives. IV. Anharmonic effects in the benzene spectrum
Authors: Maslen Paul E. , Handy Nicholas C. , Amos Roger D. , Jayatilaka Dylan 
Published: July 2002

This is the fourth in a series of papers on the ab initio calculation of the third and fourth derivatives of the energy of a molecule. In this paper we examine anharmonic effects in the infrared and Raman spectra of benzene. The following spectroscopic properties have been calculated; ab initio anharmonic corrections (ω−ν) and estimates of the harmonic frequencies ω for all 30 vibrational modes of C6H6 and C6D6, a complete set of anharmonic constants x and g for C6H6, intensities for the infrared spectrum of C6H6 up to 6148 cm−1, and anharmonic corrections to the Raman scattering factors for the fundamental modes of C6H6. In addition, we have improved on previous calculations of the equilibrium geometry of benzene, using Mo/ller–Plesset perturbation theory and a triple zeta plus double polarization (TZ2P) basis. We have also calculated a zero-point vibrationally averaged geometry which is in good agreement with the experimental R0 value. All these calculations are based on a Hartree–Fock quartic potential, cubic dipole surface, and quadratic polarizability surface, using a double-zeta plus polarization (DZP) basis. This is the first time a complete anharmonic potential has been obtained for a molecule of this size; the computer time required was minimized by the use of analytic derivative programs in favor of finite-difference programs. The quartic potential is presented in three coordinate systems.
We discuss efficient algorithms for the nonlinear transformation of the potential from normal coordinates to valence coordinates and for symmetry checking the potential. The approximations used in our calculations have been examined and we find that the use of a Hartree–Fock DZP potential together with a perturbative treatment of the vibrational Hamiltonian is just as accurate for D6h benzene as for smaller molecules. In order to examine correlation effects in the B2u modes 14 and 15, basis-set limit second-order Mo/ller–Plesset TZ2P+f harmonic frequencies have been calculated for these modes. It is suggested that, while these modes are very sensitive to correlation, anharmonicity has only a small effect, so a Hartree–Fock DZP anharmonic potential is adequate. Furthermore, experimental determination of anharmonic corrections to frequencies is very difficult for a molecule of this size so we hope our calculations will fill this gap.
Diocotron instability for intense relativistic non-neutral electron flow in planar diode geometry
Authors: Davidson Ronald C. , Tsang Kang T. , Uhm Han S. 
Published: July 2002

The extraordinary-mode eigenvalue equation is used to investigate detailed properties of the diocotron instability for sheared, relativistic electron flow in a planar diode. The theoretical model is based on the cold-fluid-Maxwell equations assuming low-frequency flute perturbations about a tenuous electron layer satisfying ω2pb(x)≪ω2c and ‖ω−kVy(x)‖2≪ω2c. The cathode is located at x=0; the anode is located at x=d; the outer boundary of the electron layer is located at x=x+b&lt;d; and the inner boundary of the layer is located at x=x−b&lt;x+b. The extraordinary-mode
eigenvalue equation is solved exactly for the case where nb(x)/ γb(x) =n̂b/γ̂b =const within the electron layer (x−b&lt;x&lt;x+b). Here, nb(x) =n̂b cosh [κ̂(x−x−b)]/ cosh[κ̂(x+b−x−b)] is the equilibrium density profile, γb (x)=cosh[κ̂(x−x−b)] is the relativistic mass factor, and ω̂D =κ̂c=4πn̂bec/B0 =const is the diocotron frequency. The analysis leads to a transcendental dispersion relation for the complex eigenfrequency ω in terms of the wavenumber k (in the flow direction), the relativistic flow parameter θ=ω̂D(x+b−x−b)/c, and the geometric factors Δi=x−b/d, Δ0=(d−x+b)/d, and Δb=(x+b−x−b)/d. It is found that the diocotron instability is completely stabilized by relativistic and electromagnetic effects whenever 2(ΔiΔ0)1/2/Δb &lt;(sinh θ)/θ, i.e., stabilization occurs whenever the flow is sufficiently relativistic (sufficiently large θ) and/or the vacuum regions are sufficiently narrow (sufficiently small Δ0 or Δi).
Effect of polyunsaturated phosphatidyl‐choline on lipid transport system in alcoholic liver injury
Authors: CHIRKIN ALEXANDER A. , KONEVALOVA NATALYA YU. , GREBENNIKOV IGOR N. , KULIKOV VYACHESLAV A. , SARAEV YURY V. , BUKO VLADYMIR U. , CHIRKINA IRINA A. , DANCHENKO ELENA O. , GUNDERMANN KARL‐J. 
Published: July 2002

AbstractThe aim of this study was to determine whether serum lipid composition and lipolytic activities in alcoholinduced liver dystrophy were modified by the co‐administration of polyunsaturated phosphatidylcholine (PPC). Chronic alcohol intoxication was induced in rats by intragastric ethanol administration of 3.5 g/kg body weight per day over 56 days. Aqueous PPC suspension was given intragastrally in doses of 100 and 300 mg/kg body weight. Chronic alcohol intoxication led to the development of protein and lipid dystrophy of hepatocytes. PPC partially prevented alcoholic injury of the liver cells and had a normalizing effect on cholesterol esterification, lipolysis of lipoproteins and on the fatty acid composition of the main lipoprotein classes.
Wound Complications Following Resection of Adductor Compartment Tumours
Authors: Grainger Melvin F. , Grimer Robert J. , Carter Simon R. , Tillman Roger M. 
Published: July 2002

Purpose Limb salvage surgery of soft tissue sarcomas is associated with both a risk of local recurrence and wound complications.
Although the lower limb appears to be at greater risk of wound‐related morbidity, few studies separate anatomical
compartments. We believe that the adductor compartment of the thigh has a particularly high rate of complications and so
performed a retrospective analysis of all soft tissue sarcomas arising in this region undergoing limb salvage.Patients Patients with intermediate and high grade adductor compartment tumours were identified from our database and
the case notes were reviewed for patient, tumour, surgical and wound variables, identifying those with wound complications
both before and after discharge.Results Of 49 patients who underwent limb salvage surgery, 22 (42.9%) developed complications. Twelve patients (24.5%)
required further surgery prior to wound healing and 10 patients had delays in post‐operative radiotherapy. There were significant
differences in the rates of preceding surgery, open biopsy performed at other centres and previous radiotherapy to this
region between the complicated and uncomplicated groups.Discussion The management of these difficult tumours carries a high rate of wound complications and requires careful planning
prior to tissue biopsy. Open biopsies should be performed by the tumour surgeon to allow easy inclusion of this site in
the definitive procedure. In previously irradiated or operated limbs, alternative strategies for wound management may need
to be considered.
Real or Imaginary? Human Metabolism through Nuclear Magnetism
Authors: Ross Brian D. 
Published: July 2002

AbstractThis account of the beginnings and later applications of the use of nuclear magnetic resonance for noninvasive medical diagnosis was presented at a Symposium held in Oxford, UK, during September 13‐15, 2000 to mark the centenary of the birth of Hans Krebs, on August 25, 1900.
Estimating the significance of sequence order in protein
secondary structure and prediction
Authors: Park Jong , Dietmann Sabine , Heger Andreas , Holm Liisa 
Published: July 2002

Abstract
Motivation: How critical is the sequence order information in predicting protein secondary structure segments? We tried to get a rough insight on it from a theoretical approach using both a prediction algorithm and structural fragments from Protein Databank (PDB).
Results: Using reverse protein sequences and PDB structural fragments, we theoretically estimated the significance of the order for protein secondary structure and prediction. On average: (1) 79% of protein sequence segments resulted in the same prediction in both normal and reverse directions, which indicated a relatively high conservation of secondary structure propensity in the reverse direction; (2) the reversed sequence prediction alone performed less accurately than the normal forward sequence prediction, but comparably high (2% difference); (3) the commonly predicted regions showed a slightly higher prediction accuracy (4%) than the normal sequences prediction; and (4) structural fragments which have counterparts in reverse direction in the same protein showed a comparable degree of secondary structure conservation (73% identity with reversed structures on average for pentamers).
Contact: jong@biosophy.org; dietmann@ebi.ac.uk; heger@ebi.ac.uk; holm@ebi.ac.uk
*** Present address: EBI, Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. To whom correspondence should be addressed.
EDIBLE: experimental design and information calculations in
phylogenetics
Authors: Massingham T. , Goldman N. 
Published: July 2002

Abstract
*Present address: University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK.
Summary: Although evolutionary inference from molecular sequences is a statistical problem, little attention has been paid to questions of experimental design. A computer program, EDIBLE, has been developed to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.
Availability: Source code (ANSI C), executables and documentation for EDIBLE are available from http://ng-dec1.gen.cam.ac.uk/info/index.htmland ‘downstream’ Web pages.
Contact: N.Goldman@gen.cam.ac.uk
Prediction of genetic structure in eukaryotic DNA using
reference point logistic regression and sequence alignment
Authors: Hooper Peter M. , Zhang Haiyan , Wishart David S. 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Motivation: Current software tools are moderately effective in predicting genetic structure (exons, introns, intergenic regions, and complete genes) from raw DNA sequence data. Improvements in accuracy and speed are needed to deal with the increasing volume of data from large scale sequencing projects.
Results: We present a two-stage computer program to predict genetic structure in eukaryotic DNA. The first stage makes use of a novel statistical technique, called reference point logistic (RPL) regression, to calculate scores for potential functional sites. These site scores are combined with interval content, length, and state scores, via a Generalized Hidden Markov Model, to determine a combined score for each possible parse of a given DNA sequence into exons, introns, and intergenic regions. An optimal parse is found using a dynamic programming algorithm. In the second stage, protein sequence alignment methods are applied to improve the accuracy of the initial parse. Computation in the first stage of the program is very fast (1 s on a 360 MHz CPU for a 16 kb sequence) and its predictive accuracy typically matches or exceeds the best results reported for other methods (Sensitivity = 0.93 and Specificity = 0.93 for the Burset/Guigótest set). Computation in the second stage is slower, but the final predictions are more accurate (Sn = 0.97, Sp = 0.97). The program (called GRPL) can handle partial, single, and multi-gene sequences. The program is also capable of predicting the genetic structure of vertebrate, invertebrate, and plant DNA with nearly equal accuracy. Statistical techniques have also been introduced to model the effects of varying C+G content in a continuous manner and to control overfitting of parameters for smaller training sets.
Availability: An academic implementation of GRPL, compiled for SUN workstations, is available by anonymous ftp from snipe.pharmacy.ualberta.ca/pub. The training and test sets used in this work, together with supplementary material, can be found at the same location. A commercial implementation is available as a component of GeneTool (BioTools Inc., http://biotools.com).
Contact: hooper@stat.ualberta.ca
RadCon: phylogenetic tree comparison and consensus
Authors: Thorley Joseph L. , Page Roderic D. M. 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Summary: RadCon is a Macintosh® program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction.
Availability: The program is free and available at http://taxonomy.zoology.gla.ac.uk/~jthorley/radcon/radcon.html.
Contact: j.l.thorley@bris.ac.uk
A cross-comparison of a large dataset of genes
Authors: Cannarozzi G. , Hallett M. T. , Norberg J. , Zhou X. 
Published: July 2002

Abstract
Summary: We make available a large cross-comparison for 16 of the completely sequenced genomes and additional eukaryotic genes. The alignments were performed at the protein level using liberal similarity bounds in order to capture as many significant alignments as possible. This dataset will be updated as new genomes become available.
Availability: The dataset is accessible at http://cbrg.inf.ethz.ch/AllAllGeneAlign.html
Contact: hallett@inf.ethz.ch
* To whom correspondence should be addressed.
EASY—an Expert Analysis SYstem for interpreting database
search outputs
Authors: Selley J. N. , Swift J. , Attwood T. K. 
Published: July 2002

Abstract
Summary: With the ever-increasing need to handle large volumes of sequence data efficiently and reliably, we have developed the EASY system for performing combined protein sequence and pattern database searches. EASY runs searches simultaneously and distils results into a concise 1-line diagnosis. By bringing together results of several different analyses, EASY provides a rapid means of evaluating biological significance, minimising the risk of inferring false relationships, for example from relying exclusively on top BLAST hits. The program has been tested using a variety of protein families and was instrumental in resolving family assignments in a major update of the PRINTS database.
Availability: http://www.bioinf.man.ac.uk/dbbrowser/easy/
Contact: selley@bioinf.man.ac.uk
* To whom correspondence should be addressed.
Detection of conserved physico-chemical characteristics of
proteins by analyzing clusters of positions with co-ordinated
substitutions
Authors: Afonnikov D. A. , Oshchepkov D. Yu. , Kolchanov N. A. 
Published: July 2002

Abstract
Motivation: It is known that the physico-chemical characteristics of proteins underlying specific folding of the polypeptide chain and the protein function are evolutionary conserved. Detection of such characteristics while analyzing homologous sequences would expand essentially the knowledge on protein function, structure, and evolution. These characteristics are maintained constant, in particular, by co-ordinated substitutions. In this process, the destabilizing effect of a substitution may be compensated by another substitution at a different position within the same protein, making the overall change in this protein characteristic insignificant. Consequently, the patterns of co-ordinated substitutions contain important information on conserved physico-chemical properties of proteins, requiring their investigation and development of the corresponding methods and software for correlation analysis of protein sequences available to a wide range of users.
Results: A software package for analyzing correlated amino acid substitutions at different positions within aligned protein sequences was developed. The approach implies searching for evolutionary conserved physico-chemical characteristics of proteins based on the information on the pairwise correlations of amino acid substitutions at different protein positions. The software was applied to analyze DNA-binding domains of the homeodomain class. As a result, two conservative physico-chemical characteristics preserved due to the co-ordinated substitutions at certain groups of positions in the protein sequence. Possible functional roles of these characteristics are discussed.
Availability: The program package is available at http://wwwmgs.bionet.nsc.ru/programs/CRASP/
Contact: ada@bionet.nsc.ru
* To whom correspondence should be addressed.
Taxonomy workbench
Authors: Wildpaner Michael , Schneider Georg , Schleiffer Alexander , Eisenhaber Frank 
Published: July 2002

Abstract
Summary: At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database.
Availability: An implementation of the taxonomy workbench is accessible for public use as a www-service at http://mendel.imp.univie.ac.at/taxonomy/. Software components for the command-line and for the www-version are available on request.
Contact: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at
Supplementary information: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html.
* To whom correspondence should be addressed.
ToolShop: prerelease inspections for protein structure
prediction servers
Authors: Rychlewski Leszek 
Published: July 2002

Abstract
Summary: The ToolShop server offers a possibility to compare a protein tertiary structure prediction server with other popular servers before releasing it to the public. The comparison is conducted on a set of 203 proteins and the collected models are compared with over 20 other programs using various assessment procedures. The evaluation lasts ca one week.
Availability: The ToolShop server is available at http://BioInfo.PL/ToolShop/. The administrator should be contacted to couple the tested server to the evaluation suite.
Contact: leszek@bioinfo.pl
Supplementary information: The evaluation procedures are similar to those implemented in the continuous online server evaluation program, LiveBench. Additional information is available from its homepage (http://BioInfo.PL/LiveBench/).
MutaProt: a web interface for structural analysis of point

mutations
Authors: Eyal Eran , Najmanovich Rafael , Sobolev Vladimir , Edelman Marvin 
Published: July 2002

Abstract
Summary: A web-based tool, termed ‘MutaProt’, is described which analyses pairs of PDB files whose members differ in one, or two, amino acids. MutaProt examines the micro environment surrounding the exchanged residue(s) and can be searched by specifying a PDB ID, keywords, or any pair of amino acids. Detailed information about accessibility of the exchanged residue(s) and its atomic contacts are provided based on CSU software (Sobolev et al. , Bioinformatics , 15, 327–332, 1999). An interactive 3D presentation of the superimposed regions around the mutation(s) is included. MutaProt is updated weekly.
Availability: http://www.bioinfo.weizmann.ac.il/MutaProt
Contact: eran.eyal@weizmann.ac.il
* To whom correspondence should be addressed.
Mixture modelling of gene expression data from microarray
experiments
Authors: Ghosh Debashis , Chinnaiyan Arul M. 
Published: July 2002

Abstract
Motivation: Hierarchical clustering is one of the major analytical tools for gene expression data from microarray experiments. A major problem in the interpretation of the output from these procedures is assessing the reliability of the clustering results. We address this issue by developing a mixture model-based approach for the analysis of microarray data. Within this framework, we present novel algorithms for clustering genes and samples. One of the byproducts of our method is a probabilistic measure for the number of true clusters in the data.
Results: The proposed methods are illustrated by application to microarray datasets from two cancer studies; one in which malignant melanoma is profiled (Bittner et al. , Nature , 406, 536–540, 2000), and the other in which prostate cancer is profiled (Dhanasekaran et al. , 2001, submitted).
Availability: Macros written in the R language implementing the methods in this report can be obtained at the first author’s website: http://www.sph.umich.edu/~ghoshd/COMPBIO/mixture1/index.html.
Contact: ghoshd@umich.edu
D-ASSIRC: distributed program for finding sequence similarities
in genomes
Authors: Vincens Pierre , Badel-Chagnon Anne , André Cécile , Hazout Serge 
Published: July 2002

Abstract
Motivation: Locating the regions of similarity in a genome requires the availability of appropriate tools such as ‘Accelerated Search for SImilar Regions in Chromosomes’ (assirc; Vincens et al. , Bioinformatics , 14, 715–725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units.
Results: The new version d-assircis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ass); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy agd) or locally managed by numerous processors (strategy ald). The result is that the strategy assis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy aldis better for a small set of processors (typically for four or six).The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes.
Availability: d-assircis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.
Contact: vincens@biologie.ens.fr
* To whom correspondence should be addressed.