bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperfine Interaction, Zeeman and Stark Effects for Excited States in Rubidium
Authors: G Belin  , L Holmgren  , S Svanberg  
Published: January 2007

Highly excitedPandDstates in87Rb were examined using a two-step excitation procedure. A conventional rf lamp and a CW dye laser were used for the first and second step, respectively. The following results for the magnetic dipole interaction constanta, the electric quadrupole interaction constantb, the LandégJfactor, and the tensor polarizability α2were obtained in level-crossing and optical-double-resonance experiments:92P3/2:a= 4.05(3) MHz,b=0.55(3) MHz,gJ= 1.3335(15)102P3/2:a= 2.60(8) MHz,gJ= 1.3332(20)82D3/2:a= 2.840(15) MHz,b= 0.17(2) MHz82D5/2:a= -1.20(15) MHz,gJ= 1.1998(15)92D3/2:a= 1.900(10) MHz,b= 0.11(3) MHz92D5/2:a= (-)0.80(15) MHz,gJ= 1.1995(15), α2= 180.3(9.0) MHz/(kV/cm)2Many-body calculations of the hyperfine structure of Rb have been performed. The polarization effect is included to all orders, whereas the correlation effect is omitted. The negativeafactors for the2D5/2states, indicating large perturbations, are explained by the polarization contribution. A review of experimental hyperfine interaction constants, LandégJfactors and tensor polarizabilities for rubidium is given together with theoretical values of theafactors. The quadrupole moment for87Rb is obtained from thebfactors for the2P3/2and2D3/2states, using quadrupole parameters from the many-body calculations. The correlation effect is included in a semi-empirical way.
Hyperfine Interaction, Zeeman and Stark Effects for Excited States in Cesium
Authors: G Belin  , L Holmgren  , S Svanberg  
Published: January 2007

Our previous measurements in thePandDseries in133Cs have been extended to a number of higher lying levels, populated in a two-step excitation process involving an rf lamp and a CW dye laser. TheDstates were studied with the level-crossing technique, while the optical-double-resonance method was used for the investigation of thePstates. For the magnetic dipole interaction constanta, the LandégJfactor, and the tensor polarizability α2we obtain122P3/2:a= 1.10(3) MHz,gJ= 1.3340(15)132P3/2:a= 0.77(5) MHz,gJ= 1.3337(20)72D3/2: |a| = 7.4(2) MHz142D3/2: |a| = 0.425(7) MHz152D3/2: |a| = 0.325(8) MHz162D3/2: |a| = 0.255(12) MHz172D3/2: |a| = 0.190(12) MHz182D3/2: |a| = 0.160(10) MHz132D5/2: α2= 19(1) GHz/(kV/cm)2142D5/2: α2= 37(2) GHz/(kV/cm)2152D5/2: α2= 70(4) GHz/(kV/cm)2162D5/2: α2= 120(6) GHz/(kV/cm)2172D5/2: α2= 199(10) GHz/(kV/cm)2182D5/2: α2= 323(16) GHz/(kV/cm)2Ab initio calculations of many-body perturbation type, including polarization effects to all orders, have been performed in order to obtain theoretical values of the hyperfine structure constants. The resultingafactors are listed together with the corresponding experimental values for mostS, P, andDstates in133Cs measured so far. The discrepancy between the experimental and theoretical values is mainly due to the omission of the correlation effect, which is essentially as important as the polarization effect. Still, for theDstates the polarization effect is large enough to yield negative values for all the2D5/2states, which is in accordance with the experimental results. Semiempirical values of theafactors have also been obtained using the Fermi-Segré-Goudsmit formula, and the results are compared with the experimental values. The measured values of α2agree well with values calculated with the Coulomb approximation due to Bates and Damgaard.
New Levels and Classifications in Fe I
Authors: U Litzén  
Published: January 2007

New 5plevels in Fe I have been found from combinations with 5sand 6sbetween 1.3 μm and 2.5 μm. 55 previously observed lines have been identified in this way, among them the strongest Fe I lines in the investigated region. All 3d64s(6D)5plevels are now well established. 7 previously known but unclassified levels and 9 new levels have tentatively been assigned to 3d7(4F)5p. The term designations are based on a parametric fit of the (d+s)7penergy matrix and on the observed intensities of the combinations with 5s.Arguments are given for changing theJ-values of the AEL levelsX2andX3and the subsequent identification of these levels with 3d83P1and3P2respectively.The line at 15 648 Å, which has been suggested for measurement of solar magnetic fields, is now classified as 5s7D1-5p7D1and its effective-gvalue can be calculated.
Rotational Analysis of the a3Π-X1Σ+Transition of AlF
Authors: I Kopp  , B Lindgren  , C Malmberg  
Published: January 2007

Thea3Π-X1Σ+transition of AlF has been observed in absorption by heating a mixture of AlF3and Al powder to approximately 1 600 K in a King type furnace. The position of theQ2head of thea3Π-X1Σ+(0, 0) band is found to be 27 254.1 cm-1or 3 668.13 Å, which is in good agreement with the value of the singlet-triplet separation determined from earlier perturbation analysis. The (0, 0) and (1, 1) bands have been rotationally analyzed. The following equilibrium values of constants (in cm-1) have been determined for theastate:Te= 27 239.4 (1) ωe= 830.3 (3) ωexe= 4.6 (2)Be= 0.55718 (3) αe= 0.00468 (5)
Spontaneous Emission of Electromagnetic Waves by a Semi-bounded Non-equilibrium Plasma
Authors: I P Yakimenko  , A G Zagorodny  
Published: January 2007

The boundary value problem of an anisotropic plasma half-space excitation by the given space-time distribution of sources is solved. The energy relations are determined for the spontaneous emission from a semi-bounded non-equilibrium plasma. The generalization of the well-known results of classical radiation theory is established (in particular, Kirchhoff's law) for the case of non-equilibrium emission from a half-space of anisotropic plasma.The quasistatic surface excitation spectra are investigated in a one-component plasma with a low-density electron beam and in a non-isothermal electron-ion plasma with electron drift relative to the ions. The possible instability of such excitations and the anomal effective temperature growth for the quasistationary part of the spontaneous field are shown. The threshold values of the electron beam velocities for various branches of the surface excitations are calculated.
A Z-Dependent Representation of the Transition Integral
Authors: Charlotte Froese Fischer  
Published: January 2007

It is shown that transition integrals for sodium isoelectronic sequences can be represented accurately by expressions of the formwhereI0is the value for hydrogen, ands0,s1,...,s4are parameters. In most instances the errors are less than 0.5%. Such formulas facilitate the study of trends inf-values for transitions or life-times of excited levels.
Software package for automatic microarray image analysis (MAIA)
Authors: Novikov Eugene , Barillot Emmanuel 
Published: January 2007

AbstractSummary: Although various software solutions are currently available for microarray image analysis, one would still expect to develop algorithms ensuring higher level of intelligence and robustness. We present a fully functional software package for automatic processing of the two-color microarray images including spot localization, quantification and quality control. The developed algorithms aim at making ratio estimates more resistant to array contamination and offer automatic tools to evaluate spot quality.Availability: A demo version of the software can be downloaded from http://bioinfo.curie.fr/projects/maia. A full version is freely available to non-commercial users upon request from the authors.Contact: eugene.novikov@curie.fr
Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search
Authors: Dutta Debojyoti , Chen Ting 
Published: January 2007

AbstractMotivation: Due to the recent advances in technology of mass spectrometry, there has been an exponential increase in the amount of data being generated in the past few years. Database searches have not been able to keep with this data explosion. Thus, speeding up the data searches becomes increasingly important in mass-spectrometry-based applications. Traditional database search methods use one-against-all comparisons of a query spectrum against a very large number of peptides generated from in silico digestion of protein sequences in a database, to filter potential candidates from this database followed by a detailed scoring and ranking of those filtered candidates.Results: In this article, we show that we can avoid the one-against-all comparisons. The basic idea is to design a set of hash functions to pre-process peptides in the database such that for each query spectrum we can use the hash functions to find only a small subset of peptide sequences that are most likely to match the spectrum. The construction of each hash function is based on a random spectrum and the hash value of a peptide is the normalized shared peak counts score (cosine) between the random spectrum and the hypothetical spectrum of the peptide. To implement this idea, we first embed each peptide into a unit vector in a high-dimensional metric space. The random spectrum is represented by a random vector, and we use random vectors to construct a set of hash functions called locality sensitive hashing (LSH) for preprocessing. We demonstrate that our mapping is accurate. We show that our method can filter out &gt;95.65% of the spectra without missing any correct sequences, or gain 111 times speedup by filtering out 99.64% of spectra while missing at most 0.19% (2 out of 1014) of the correct sequences. In addition, we show that our method can be effectively used for other mass spectra mining applications such as finding clusters of spectra efficiently and accurately.Contact: tingchen@usc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs
Authors: Song Young C. , Kawas Edward , Good Ben M. , Wilkinson Mark D. , Tebbutt Scott J. 
Published: January 2007

AbstractSummary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual ‘surfing’, to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future.Availability: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.Contact: stebbutt@mrl.ubc.caSupplementary information: Additional information, including test result data, is available from the iCAPTURE Centre web site (see above).
ProServer: a simple, extensible Perl DAS server
Authors: Finn Robert D. , Stalker James W. , Jackson David K. , Kulesha Eugene , Clements Jody , Pettett Roger 
Published: January 2007

AbstractSummary: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols for the exchange mechanism must be developed. One such data exchange protocol that is widely used is the Distributed Annotation System (DAS). For example, DAS has enabled small experimental groups to integrate their data into the Ensembl genome browser. We have developed ProServer, a simple, lightweight, Perl-based DAS server that does not depend on a separate HTTP server. The ProServer package is easily extensible, allowing data to be served from almost any underlying data model. Recent additions to the DAS protocol have enabled both structure and alignment (sequence and structural) data to be exchanged. ProServer allows both of these data types to be served.Availability: ProServer can be downloaded from http://www.sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/. Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/.Contact: rmp@sanger.ac.ukSupplementary Materials: DasClientExamples.pdf
On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins
Authors: Park Yungki , Helms Volkhard 
Published: January 2007

AbstractHelical membrane proteins (HMPs) play a crucial role in diverse physiological processes. Given the difficulty in determining their structures by experimental techniques, it is desired to develop computational methods for predicting the burial status of transmembrane residues. Deriving a propensity scale for the 20 amino acids to be exposed to the lipid bilayer from known structures is central to developing such methods. A fundamental problem in this regard is what would be the optimal way of deriving propensity scales. Here, we show that this problem can be reformulated such that an optimal scale is straightforwardly obtained in an analytical fashion. The derived scale favorably compares with others in terms of both algorithmic optimality and practical prediction accuracy. It also allows interesting insights into the structural organization of HMPs. Furthermore, the presented approach can be applied to other bioinformatics problems of HMPs, too.All the data sets and programs used in the study and detailed primary results are available upon request.Contact: volkhard.helms@bioinformatik.uni-saarland.de
A new protein–protein docking scoring function based on interface residue properties
Authors: Bernauer J. , Azé J. , Janin J. , Poupon A. 
Published: January 2007

AbstractMotivation: Protein–protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein–protein docking procedure traditionally consists of two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them.Results: To address the second step, we developed a scoring function based on a Voronoï tessellation of the protein three-dimensional structure. We showed that the Voronoï representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein–protein complexes and on decoys, and used them as attributes in several statistical learning procedures: a logistic function, Support Vector Machines (SVM), and a genetic algorithm. For the later, we used ROGER, a genetic algorithm designed to optimize the area under the receiver operating characteristics curve. To further test the scores derived with ROGER, we ranked models generated by two different docking algorithms on targets of a blind prediction experiment, improving in almost all cases the rank of native-like solutions.Availability: http://genomics.eu.org/spip/-Bioinformatics-tools-
Biskit—A software platform for structural bioinformatics
Authors: Grünberg Raik , Nilges Michael , Leckner Johan 
Published: January 2007

AbstractSummary: Biskit is a modular, object-oriented python library that provides intuitive classes for many typical tasks of structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes and molecular dynamics trajectories. At the same time, Biskit offers a software platform for the rapid integration of external programs and new algorithms into complex structural bioinformatics workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, Prosa, Hmmer and Modeller; interfaces to further software can be easily added. Moreover, Biskit simplifies the parallelization of time consuming calculations via PVM (Parallel Virtual Machine).Availability: The latest snapshot of Biskit, documentation and examples are freely available under the GNU General Public License at http://biskit.sf.net (alternate url http://biskit.pasteur.fr).Contact: johan.leckner@nmr.se, raik.gruenberg@crg.es
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
Authors: Blom Evert-Jan , Bosman Dinne W. J. , van Hijum Sacha A. F. T. , Breitling Rainer , Tijsma Lars , Silvis Remko , Roerdink Jos B. T. M. , Kuipers Oscar P. 
Published: January 2007

AbstractSummary: FIVA (Function Information Viewer and Analyzer) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software assists in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes.Availability: http://bioinformatics.biol.rug.nl/standalone/fiva/Contact: o.p.kuipers@rug.nlSupplementary information: http://bioinformatics.biol.rug.nl/standalone/fiva/suppMaterials.php
The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
Authors: Keibler Evan , Arumugam Manimozhiyan , Brent Michael R. 
Published: January 2007

AbstractMotivation: Hidden Markov models (HMMs) and generalized HMMs been successfully applied to many problems, but the standard Viterbi algorithm for computing the most probable interpretation of an input sequence (known as decoding) requires memory proportional to the length of the sequence, which can be prohibitive. Existing approaches to reducing memory usage either sacrifice optimality or trade increased running time for reduced memory.Results: We developed two novel decoding algorithms, Treeterbi and Parallel Treeterbi, and implemented them in the TWINSCAN/N-SCAN gene-prediction system. The worst case asymptotic space and time are the same as for standard Viterbi, but in practice, Treeterbi optimally decodes arbitrarily long sequences with generalized HMMs in bounded memory without increasing running time. Parallel Treeterbi uses the same ideas to split optimal decoding across processors, dividing latency to completion by approximately the number of available processors with constant average overhead per processor. Using these algorithms, we were able to optimally decode all human chromosomes with N-SCAN, which increased its accuracy relative to heuristic solutions. We also implemented Treeterbi for Pairagon, our pair HMM based cDNA-to-genome aligner.Availability: The TWINSCAN/N-SCAN/PAIRAGON open source software package is available from http://genes.cse.wustl.edu.Contact: brent@cse.wustl.edu
Structure-based evaluation ofin silicopredictions of protein–protein interactions using Comparative Docking
Authors: Cockell Simon J. , Oliva Baldo , Jackson Richard M. 
Published: January 2007

AbstractMotivation: Due to the limitations in experimental methods for determining binary interactions and structure determination of protein complexes, the need exists for computational models to fill the increasing gap between genome sequence information and protein annotation. Here we describe a novel method that uses structural models to reduce a large number of in silico predictions to a high confidence subset that is amenable to experimental validation.Results: A two-stage evaluation procedure was developed, first, a sequence-based method assessed the conservation of protein interface patches used in the original in silico prediction method, both in terms of position within the primary sequence, and in terms of sequence conservation. When applying the most stringent conditions it was found that 20.5% of the data set being assessed passed this test. Secondly, a high-throughput structure-based docking evaluation procedure assessed the soundness of three dimensional models produced for the putative interactions. Of the data set being assessed, 8264 interactions or over 70% could be modelled in this way, and 27% of these can be considered ‘valid’ by the applied criteria. In all, 6.9% of the interactions passed both the tests and can be considered to be a high confidence set of predicted interactions, several of which are described.Availability: http://bioinformatics.leeds.ac.uk/~bmb4sjcContact: r.m.jackson@leeds.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Computing exactP-values for DNA motifs
Authors: Zhang Jing , Jiang Bo , Li Ming , Tromp John , Zhang Xuegong , Zhang Michael Q. 
Published: January 2007

AbstractMotivation: Many heuristic algorithms have been designed to approximate P-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown.Results: We show the problem to be NP-hard, and present MotifRank, software based on dynamic programming, to calculate exact P-values of motifs. We define the exact P-value on a general and more precise model. Asymptotically, MotifRank is faster than the best exact P-value computing algorithm, and is in fact practical. Our experiments clearly demonstrate that MotifRank significantly improves the accuracy of existing approximation algorithms.Availability: MotifRank is available from http://bio.dlg.cnContact: mzhang@cshl.edu mli@uwaterloo.caSupplementary information: Supplementary data are available at Bioinformatics online.
Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models
Authors: Matsui Shigeyuki , Ito Masaaki , Nishiyama Hiroyuki , Uno Hajime , Kotani Hirokazu , Watanabe Jun , Guilford Parry , Reeve Anthony , Fukushima Masanori , Ogawa Osamu 
Published: January 2007

AbstractMotivation: The development of gene expression microarray technology has allowed the identification of differentially expressed genes between different clinical phenotypic classes of cancer from a large pool of candidate genes. Although many class comparisons concerned only a single phenotype, simultaneous assessment of the relationship between gene expression and multiple phenotypes would be warranted to better understand the underlying biological structure.Results: We develop a method to select genes related to multiple clinical phenotypes based on a set of multivariate linear regression models. For each gene, we perform model selection based on the doubly-adjusted R-square statistic and use the maximum of this statistic for gene selection. The method can substantially improve the power in gene selection, compared with a conventional method that uses a single model exclusively for gene selection. Application to a bladder cancer study to correlate pre-treatment gene expressions with pathological stage and grade is given. The methods would be useful for screening for genes related to multiple clinical phenotypes.Availability: SAS and MATLAB codes are available from author upon request.Contact: matsui@pbh.med.kyoto-u.ac.jp