bluuebunny/crossref_metadata_2025_split huggingface dataset:
The visible excitation spectrum of jet cooled NO2: Statistical analysis of rovibronic interactions
Authors: Delon Antoine , Georges Robert , Jost Rémy 
Published: July 2002

We have recorded the high resolution (150 MHz) excitation spectra of NO2 molecules cooled in a supersonic jet in two energy ranges: 16 000–19 362 cm−1 [‘‘yellow’’ range, see R. Georges, A. Delon, and R. Jost, J. Chem. Phys. 103, 1732 (1995), hereafter referred to as paper I] and 23 326–23 945 cm−1 (‘‘blue’’ range). In this paper we are interested mainly in the rovibronic properties of about 1500 rotational levels (N=1, K=0, J=1/2, and J=3/2) observed in these two ranges. Among these levels about 480 are observed via the so-called extra lines, i.e., the lines which are observable because of rovibronic couplings between bright levels (N=1, K=0, 2B2 vibronic character) and nearby dark levels. These rovibronic couplings result mainly from second order spin–orbit and orbit–rotation interactions which have been evidenced previously by Zeeman effect and anticrossing experiments [A. Delon, P. Dupré, and R. Jost, J. Chem. Phys. 99, 9482 (1993)]. By comparing the average matrix element of rovibronic interactions occuring for N=1, K=0 (J=1/2 and J=3/2), and for N=3, K=0 (J=5/2 and J=7/2) we can exclude a significant contribution from Coriolis interactions.
A model of small random matrices constructed by using the properties of the above mentioned rovibronic Hamiltonian (density of states, selection rules, and matrix elements) allowed us to reproduce the observed statistical properties of the rovibronic states: average number of extra lines per vibronic band, distribution of intensities, Fourier transform analysis, next-neighbor spacing distribution, hierarchical tree analysis, and intensity and energy correlations between J=1/2 and J=3/2 lines. All these properties confirm that the second-order spin–orbit interaction is responsible for most of the observed extra lines for low rotational levels N=1 and N=3, K=0. As a result, the average reduced rovibronic matrix element is 0.6∓0.1 cm−1 and 0.7∓0.1 cm−1 for the yellow and blue ranges, respectively. The yellow range result is in reasonable agreement with the results obtained previously under magnetic field experiments. We also derive analytical formulas applicable for the weak interaction regime and discuss the relation between the observed distribution of matrix elements and the true distribution.
Berry phases and unitary transformations
Authors: Jordan Thomas F. 
Published: July 2002

Berry phases for spin are defined for any closed loop made by a vector changing direction in three-dimensional space. A sequence of rotations moves the vector along the loop. Each rotation is around the axis perpendicular to the moving vector. The Berry phases come from the eigenvalues of the unitary operator for the product of these rotations. The angle of the product rotation is shown to be the solid angle enclosed by the loop. The proof uses the ordinary language of quantum mechanics. The product is calculated from the commutation relations for spin. A general framework is set up to define Berry phases for other transformations and states like those for rotations and spin. The integral formula is derived. Alternatives for dynamics are shown to provide different applications and interpretations of the same mathematics. An example is used to show how one Hamiltonian may be simpler than others. Adiabatic evolution is obtained in the limit as a coupling constant goes to zero, so the adiabatic changes are made by a weak perturbation that acts over a long time. The Berry phase is the same whether the coupling constant is large or small. A rationale for the definition of Berry phases is obtained from any of the alternatives for dynamics. It is particularly clear in both the limit of adiabatic evolution, where the Hamiltonian does not contain the operator that generates Berry phases, and the opposite extreme where the Hamiltonian is the operator that generates Berry phases. The latter is illustrated with an example for spin. The general definition of Berry phases and the method of calculating them are illustrated by obtaining Berry phases from Lorentz transformations. They are similar to those obtained from rotations. A vector traces a loop on a unit hyperboloid instead of the unit sphere. In place of the solid angle, the Berry phases contain the analogous measure of the area enclosed by the loop on the hyperboloid.
The sign is opposite what it is for rotations. The general definition is shown to fit any unitary representation of a semisimple Lie group. The complete set of commuting operators is chosen to contain a basis for a Cartan subalgebra of the Lie algebra of generators. If a sequence of transformations by unitary operators in the group representation takes each operator in the Cartan subalgebra around a loop in the Lie algebra back to the same operator, it can be made by unitary operators in the group representation that have all the properties required for the definition of Berry phases. The loops are made by vectors moving in a real space, the Lie algebra. The motion of the vectors must maintain the lengths and angles defined by the Cartan metric of the Lie algebra. The Berry phases are determined by one loop made by one suitably chosen operator from the Cartan subalgebra.
Surgical Treatment of Chondrosarcoma of the Sternum
Authors: Ashford Robert U. , Stanton Jeremy , Khan Farid , Pringle Jean A. S. , Cannon Stephen R. , Briggs Timothy W. R. 
Published: July 2002

Purpose: We reviewed all tumours of the sternum referred to The London Bone and Soft Tissue Tumour Service between
1956 and 1997 inclusive.Patients and results: There were eight patients with this pathology, the male to female ratio was 3:1 and their mean age was
53 years. Of these patients, three are alive and disease free, one is alive with recurrence, and four have died, two of the consequences
of the disease and two of unrelated causes. Surgery is the principal treatment of these tumours both for excision and
subsequent reconstruction.Discussion: Extended disease‐free survival is possible with correct diagnosis, complete excision at the first operation, appropriate
skeletal reconstruction, adequate skin cover and appropriate postoperative support and follow‐up.
The Clinical Value of Flow Cytometric DNA Content Analysis in Patientswith Soft Tissue Sarcomas
Authors: Samur Mustafa , Pamir Ali , Akbulut Hakan , Erekul Selim , Sağlik Yener , Yildiz Yusuf , Dinçol Dilek , Içli Fikri 
Published: July 2002

Purpose. The purpose of this study was to evaluate: (1) the correlation
between grade and ploidy or S‐phase fraction (SPF), (2) the prognostic value of DNA flow
cytometric study in soft tissue sarcomas.Patients /Methods. In all, 47 tissue samples from soft tissue sarcoma
patients, surgically treated in the same center, were included. Flow cytometric analyses
were performed according to a modified version of the original method of Hedley et al.Results. DNA ploidy status could be determined in 44 samples out of
47 (success rate 94%). Of these 44, S‐phase fraction could be calculated in 34 samples (77%).
In the study group as a whole, aneuploidy was significantly correlated with high grade.
Survival analyses were carried out in 21 patients with soft tissue sarcoma, all surgically
treated in the same center, without chemotherapy or radiotherapy. In univariate analyses,
DNA ploidy was found to be a significant factor for overall survival (OAS) and metastasis‐free
survival MFS. Mean OAS for aneuploid tumors and diploid tumors were 35 and 65
months (p=0.034), and mean MFS 23 and 61 months, respectively (p=0.005) .Discussion.There is a relation between histological grade and ploidy in
soft tissue sarcomas. It appears that low‐grade tumors are generally diploid, whereas
high‐grade tumors tend to be aneuploid. In a subgroup of patients treated only with
surgery, DNA ploidy was found to be an important factor for predicting OAS and MFS.
Primary Chondroblastic Osteosarcoma of the Lung
Authors: Wagner Monica S. , Reyes Cesar V. 
Published: July 2002

Purpose. Primary extra‐osseous osteosarcomas are uncommon
lesions, and those originating within the lung are especially rare, with few case reports
existing in the literature.Patient. We report the case of a 48‐year‐old male smoker with a primary
osteosarcoma of the right lower lung lobe.Results. Diagnosis was based on histopathological findings of a poorly
differentiated sarcoma with malignant cellular components of osteoid and chondroid matrix,
along with immunohistochemical and electron microscopy confirmation.
Extensive clinical and radiographic evaluation failed to reveal any tumor at other anatomical
sites.
FORESST: fold recognition from secondary structure predictions of proteins.
Authors: Di Francesco V , Munson P J , Garnier J 
Published: July 2002

Abstract
MOTIVATION: A method for recognizing the three-dimensional fold from the protein amino acid sequence based on a combination of hidden Markov models (HMMs) and secondary structure prediction was recently developed for proteins in the Mainly-Alpha structural class. Here, this methodology is extended to Mainly-Beta and Alpha-Beta class proteins. Compared to other fold recognition methods based on HMMs, this approach is novel in that only secondary structure information is used. Each HMM is trained from known secondary structure sequences of proteins having a similar fold. Secondary structure prediction is performed for the amino acid sequence of a query protein. The predicted fold of a query protein is the fold described by the model fitting the predicted sequence the best. RESULTS: After model cross-validation, the success rate on 44 test proteins covering the three structural classes was found to be 59%. On seven fold predictions performed prior to the publication of experimental structure, the success rate was 71%. In conclusion, this approach manages to capture important information about the fold of a protein embedded in the length and arrangement of the predicted helices, strands and coils along the polypeptide chain. When a more extensive library of HMMs representing the universe of known structural families is available (work in progress), the program will allow rapid screening of genomic databases and sequence annotation when fold similarity is not detectable from the amino acid sequence. AVAILABILITY: FORESST web server at http://absalpha.dcrt.nih.gov:8008/ for the library of HMMs of structural families used in this paper. FORESST web server at http://www.tigr.org/ for a more extensive library of HMMs (work in progress). CONTACT: valedf@tigr.org; munson@helix.nih.gov; garnier@helix.nih.gov
A proposal for a standard CORBA interface for genome maps.
Authors: Barillot E , Leser U , Lijnzaad P , Cussat-Blanc C , Jungfer K , Guyon F , Vaysseix G , Helgesen C , Rodriguez-Tom√© P 
Published: July 2002

Abstract
MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: manu@infobiogen.fr, tome@ebi.ac.uk
Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm.
Authors: Mallios R R 
Published: July 2002

Abstract
MOTIVATION: The identification of T-cell epitopes can be crucial for vaccine development. An epitope is a peptide segment that binds to both a T-cell receptor and a major histocompatibility complex (MHC) molecule. Predicting which peptide segments bind MHC molecules is the first step in epitope prediction. RESULTS: An iterative stepwise discriminant analysis meta-algorithm explores a large molecular database to derive quantitative motifs for peptide binding. The applications presented here demonstrate the algorithm's versatility by producing four closely related models for HLA-DR1. Two models use an expert initial estimate and two do not; two models use amino acid residues as the only predictors and two use amino acid groupings as additional predictors. Each model correctly classifies &gt;90% of the peptides in the database. AVAILABILITY: Software is available commercially; data are free over the Internet.
A space-efficient algorithm for aligning large genomic

sequences
Authors: Morgenstern Burkhard 
Published: July 2002

Abstract
Summary: In the segment-by-segment approach to sequence alignment, pairwise and multiple alignments are generated by comparing gap-free segments of the sequences under study. This method is particularly efficient in detecting local homologies, and it has been used to identify functional regions in large genomic sequences. Herein, an algorithm is outlined that calculates optimal pairwise segment-by-segment alignments in essentially linear space.
Availability: The program is available at the Bielefeld Bioinformatics Server (BiBiServ) at http://bibiserv.techfak.uni-bielefeld.de/dialign/
Contact: morgenstern@mips.biochem.mpg.de
A collection of well characterised integral membrane proteins
Authors: Möller Steffen , Kriventseva Evgenia V. , Apweiler Rolf 
Published: July 2002

Abstract
Summary: A collection of transmembrane proteins with annotated transmembrane regions, for which good experimental evidence exist, was created as a test or training set for algorithms to predict transmembrane regions in proteins.
Availability: ftp://ftp.ebi.ac.uk/databases/testsets/transmembrane
Contact: moeller@ebi.ac.uk
A case study in genome-level fragment assembly
Authors: Chen Ting , Skiena Steven S. 
Published: July 2002

Abstract
Motivation: We use the fact of two teams independently sequencing the one megabase genome of Borrelia burgdorferi as an opportunity to study the accuracy of genome-level assembly.
Results: We compare the results of three different assembly programs (PHRAP, TIGR Assembler, and STROLL) on the DNA fragments used in both the Brookhaven and TIGR sequencing projects. We also describe the algorithms and data structures used in our assembly program STROLL, which was used in the Brookhaven Borrelia project.
Availability: http://genetics.med.harvard.edu/~tchen/STROLL.
Contact: tchen@arep.med.harvard.eduand skiena@cs.sunysb.edu.
Object-oriented parsing of biological databases with Python
Authors: Ramu Chenna , Gemünd Christine , Gibson Toby J. 
Published: July 2002

Abstract
Motivation: While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way.
Results: We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.
Availability: The modules are available at http://shag.embl-heidelberg.de:8000/Biopy/
Contact: chenna@embl-heidelberg.de
Supplementary information: http://shag.embl-heidelberg.de:8000/Biopy/
* To whom correspondence should be addressed.
Profiles from structure based sequence alignment of porins can
identify β stranded integral membrane proteins
Authors: Gnanasekaran T. V. , Peri Suraj , Arockiasamy A. , Krishnaswamy S. 
Published: July 2002

Abstract
Supplementary information: http://gene.tn.nic.in/sk/profiles/
Contact: krishna@mrna.tn.nic.in
To whom correspondence should be addressed.
A Web interface generator for molecular biology programs in
Unix
Authors: Letondal Catherine 
Published: July 2002

Abstract
Motivation: Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration.
Results: The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.
Availability: The program is freely available over the Internet at the following URL: http://www.pasteur.fr/~letondal/Pise/.
Contact: pise@pasteur.fr
Segmentation of long genomic sequences into domains with
homogeneous composition with BASIO software
Authors: Ramensky Vasily E. , Makeev Vsevolod Ju. , Roytberg Mikhail A. , Tumanyan Vladimir G. 
Published: July 2002

Abstract
Summary: We present a software system BASIO that allows one to segment a sequence into regions with homogeneous nucleotide composition at a desired length scale. The system can work with arbitrary alphabet and therefore can be applied to various (e.g. protein) sequences. Several sequences of complete genomes of eukaryotes are used to demonstrate the efficiency of the software.
Availability: The BASIO suite is available for non-commercial users free of charge as a set of executables and accompanying segmentation scenarios from http://www.imb.ac.ru/compbio/basio. To obtain the source code, contact the authors.
Contact: basio@imb.ac.ru; ramensky@imb.ac.ru; makeev@imb.ac.ru
* To whom correspondence should be addressed.
ORI-GENE: gene classification based on the evolutionary tree
Authors: Mizuno Hideaki , Tanaka Yoshimasa , Nakai Kenta , Sarai Akinori 
Published: July 2002

Abstract
Motivation: Genome projects have produced large amounts of data on the sequences of new genes whose functions are as yet unknown. The functions of new genes are usually inferred by comparing their sequences with those of known genes, but evaluation of the sequence homology of individual genes does not make the most of the available sequence information. Therefore, new methods and tools for extracting more biological information from homology searches would be advantageous.
Results: We have developed a computational tool, ORI-GENE, to analyze the results of sequence homology searches from the perspective of the evolution of selected sets of new genes. ORI-GENE has a graphical interface and accomplishes two important tasks: first, based on the output of homology searches, it identifies species with similar genes and displays their pattern of distribution on the phylogenetic tree. This function enables one to infer the way in which a given gene may have propagated among species over time. Second, from the distribution patterns, it predicts the point at which a given gene may have been first acquired (i.e. its ‘origin’), then classifies the gene on that basis. Because it makes use of available evolutionary information to show the way in which genes cluster among species, ORI-GENE should be an effective tool for the screening and classification of new genes revealed by genome analysis.
Availability: ORI-GENE is retrievable via the Internet at: http://www.rtc.riken.go.jp/jouhou/ORI-GENE.
Contact: hideaki.mizuno@roche.com; sarai@rtc.riken.go.jp
* To whom correspondence should be addressed.
4 Present address: Nippon Roche Research Center, 200 Kajiwara, Kamakura, Kanagawa 249-8530, Japan.
MOSAIC: segmenting multiple aligned DNA sequences
Authors: André Cécile , Vincens Pierre , Boisvieux Jean-François , Hazout Serge 
Published: July 2002

Abstract
Summary: MOSAIC is a set of tools for the segmentation of multiple aligned DNA sequences into homogeneous zones. The segmentation is based on the distribution of mutational events along the alignment. As an example, the analysis of one repeated sequence belonging to the subtelomeric regions of the yeast genome is presented.
Availability: Free access from ftp://ftp.biomath.jussieu.fr/pub/papers/MOSAIC
Contact: can@biomath.jussieu.fr
* To whom correspondence should be addressed.
Physical mapping with automatic capture of hybridization data
Authors: Hall David , Bhandarkar Suchendra M. , Arnold Jonathan , Jiang Tongzhang 
Published: July 2002

Abstract
Motivation: Contig maps are a type of physical map that show the native order of a set of overlapping genomic clones. Overlaps between clones can be detected by finding common sequences using a number of experimental protocols including hybridization of probes. All current mapping algorithms of which we are aware require that hybridizations be scored using a fixed number of discrete values (typically 0/1 or high/medium/low). When hybridization data is captured automatically using digital equipment, this provides the opportunity for hybridization intensities to be used in map construction. More fine-grained distinctions in the levels of hybridization may be exploited by algorithms to generate more accurate physical maps.
Results: We describe an approach to creating contig maps that uses measured hybridization intensities instead of data scored with a fixed number of discrete values. We describe and compare four algorithms for creating physical maps with hybridization intensities. Simulations using measured intensities sampled from actual data on Aspergillus nidulans indicate that using hybridization intensities rather than data that is automatically scored with respect to threshold values may yield more accurate physical maps.
Availability: All software programs described in this paper may be obtained by contacting the authors.
Contact: suchi@cs.uga.edu
* To whom correspondence should be addressed.