bluuebunny/crossref_metadata_2025 huggingface dataset:
Mössbauer Studies of Fe2As
Authors: P Raj  , S K Kulshreshtha
Published: January 2007

Mössbauer spectra of the antiferromagnetic compound Fe2As have been recorded at various temperatures and the eigenvalues for the nuclear excited state are derived from the least square fitted Mössbauer spectra. The nuclear Hamiltonian matrix has been solved for different ratios of the magnetic and axially-symmetric quadrupole interaction (for both positive and negative efg values) and with varying relative orientation between them. By comparing the experimental eigenvalues with those obtained by solving the above matrix, it is shown that the quadrupole interaction does not show any discontinuity near the magnetic transition temperature and the sign of efg is negative. Further at temperatures close toTN, the spins almost lie in the C-plane. As the temperature is lowered, the spins gradually rotate from the basal plane and make an angle of ∼ 16° at liquid nitrogen temperature. These observations are different from the previously reported Mössbauer results. The observed values of the chemical isomeric shift and the hyperfine field at the two sites have been discussed in relation to their known magnetic moment values.
Transition Probabilities of the 9/2+ → 7/2+ Transitions in Odd-mass Ag Isotopes
Authors: L-G Svensson  , O Bergman  , A Bäcklin  , N-G Jonsson  , J Lindskog
Published: January 2007

Conversion electrons from the 9/2+ → 7/2+ transitions in the odd-mass 105,107,111Ag nuclei have been studied in the radioactive decays of 105Cd, 107Cd and 111Pd, respectively. E2/M1 ratios have been deduced for these transitions and the half-lives of corresponding levels in 105,111Ag have been measured by means of the delayed coincidence technique. The reduced E2 transitions probabilities are compared with theoretical predictions.
The Life-time Measurements of Some High-spin States in the 138,139Ce and 141,142Nd Nuclei
Authors: J Ludziejewski  , J Bialkowski  , Z Haratym  , L-E de Geer  , A Kerek  , J Kozyczkowski
Published: January 2007

A search for high-spin isomeric states in the 138,139Ce anc 141,142Nd nuclei has been made using (α, xn) reactions and the intrinsic pulsing of the 225-cm Stockholm cyclotron. In 138Ce, besides the known 7- isomeric state at 2 128.8 keV, another one at 3 538.5 keV, 10+, with T
1/2 = (78 ± 5) ns has been found. In 139Ce a new isomeric state at 2 631.5 keV, 19/2-, with T
1/2 = (70 ± 5) ns has been identified. Also in 141Nd a high-spin isomeric level exists probably at 3 104.9 keV with T
1/2 = (26 ± 5) ns. In 142Nd the level at 3 453.0 keV, with spin I = 6, shows a half-life T
1/2 = (1.3 ± 0.1) ns while that at 4 718.5 keV, I = 8, decays with a half-life of about 0.8 ns. The time distributions in 142Nd show that the 3 242.9 keV, I = 7, or the 3 456.2 keV, I = 8, level is also delayed and decays with T
1/2 = (1.6 ± 0.1) ns. The deduced transition probabilities are compared to theoretical predictions.
Nuclear Spins of Some Neutron-deficient As Isotopes
Authors: H A Helms  , W Hogervorst  , G J Zaal  , J Blok
Published: January 2007

The nuclear spins of some neutron-deficient arsenic isotopes have been measured using the atomic beam magnetic resonance technique. The results are:72As (26.0 h)I= 2,71As (64.8 h)I= 5/2,70As (53.0 min)I= 4 and69As (15 min)I= 5/2. The spin values are compared with predictions from spectroscopic and theoretical studies.
Lifetime Broadening and CI-Resonances Observed in ESCA
Authors: S Svensson  , N Mårtensson  , E Basilier  , P Aå Malmquist  , U Gelius  , K Siegbahn
Published: January 2007

The electron spectrum of the M
2 and M
3 levels in bromine and krypton have been studied by high resolution ESCA. The M
1
M
2,3
M
2,3 super Coster-Kronig transitions become energetically forbidden for Zless than sim-36 (Kr) and recent calculations therefore predict a decrease in the M
2 and M
3 natural linewidths around krypton in the periodic system. The experiment shows that the 3p
3/2 linewidth is smaller in Kr than in Br. It is, however, also found that this decrease in linewidth is followed by configuration interaction (CI) between 3p
2
P and 3d
2
nl*2
P states. Several descrete CI resonances are observed in the Kr 3p spectrum. Such resonances are also studied in the N shell for the elements from Te (Z = 52) to Ba (Z = 56). For these elements the effect is found to be much larger due to the strong collective character of 4d-nf* excitations.
Strong Dynamical Effects of Many-Electron Interactions in Photoelectron Spectra from 4s and 4p Core Levels
Authors: G Wendin  , M Ohno
Published: January 2007

Dipolar fluctuations of 4sand 4pholes in the elements around Xe have been found to make a one-electron type of picture break down. This explains the failure of monopole relaxation, as included e.g. through the relativistic Hartree-Fock ΔSCF procedure, and shake off processes to describe ESCA spectra in this energy region. In Xe we find that neither a 4p1/2nor a 4p3/2hole can exist as an elementary excitation (quasi-stationary state) but become smeared over a large energy range. Instead, the most stable and probable state is found to belong to the Xe+(4d84f)3/2configuration and we identify this with the main ESCA peak at 145.5 eV. We also present a photo-electron spectrum for the 4sand "4p" region in quite good agreement with experiment.
The Wavelength Stability of the Resonance Line of Xenon (XeI, λ147 nm)
Authors: L Causton  , G H C Freeman  , Freda Freshwater
Published: January 2007

The variation of wavelength of the natural xenon line λ147 nm has been measured as a function of xenon pressure (10-10 to 10-4 torr) and discharge current (10 to 50 mA DC) in a lamp which has a limited discharge depth of 8 mm behind the window. Any variations with source conditions that are present are less than ±4 fm (0.04 mÅ) or 2.7 parts in 108. At higher pressures the line becomes asymmetrical.
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)
Parametric Decay of Whistler Waves
Authors: J G Turner  , T J M Boyd
Published: January 2007

The Lagrangian approach to non-linear wave interactions is applied to study the parametric decay of whistlers. These waves may decay into either an electron plasma wave together with an ion-acoustic wave or into a backward propagating whistler and an ion-acoustic wave. Growth rates and thresholds are obtained and compared with observed values.
Experimental Findings Concerning Cavity-assisted Resonances in Stringed Instruments with a Soundpost
Authors: Carl Hugo Ågren
Published: January 2007

The interaction of wood structure and air cavity near the frequency of the rigid-wall air cavity resonance is investigated. It is experimentally and theoretically shown that a string instrument body produces not one but two cavity-assisted resonances, straddling the rigid-wall cavity resonance in frequency even though both do not always form in practice. The frequencies of these two resonances are also influenced by plate tuning, and the formation of double resonances is in agreement with the electronic model proposed by John Schelleng. The double peak formation is further illustrated with a pilot experiment.
Correlations between Atmospheric Variables and Cosmic-ray Particle Fluxes
Authors: J J Torsti  , E Valtonen
Published: January 2007

Changes in cosmic-ray muon and nucleon fluxes caused by variations in atmospheric conditions were investigated theoretically and experimentally. The theory was based on the strong bootstrap version of the statistical thermodynamic model for the nucleon-nucleus collisions. A new multiplicity function was introduced in the model. This function takes into account the kinematic limitations stated by the inclusive produced particles for the mass of the parent fireball and allows the production of light hadrons with different masses. The computed predictions for the regression coefficients describing changes in muon fluxes at sea level are in satisfactory agreement with experimental values obtained by means of a scintillator telescope and radio-sonde measurements.
Levels in25Mg
Authors: J E Christiansson  , J Dubois  , H Roth  , L Jarneborn
Published: January 2007

The reactions22Ne(α,nγ)25Mg and24Mg(d,pγ)25Mg have been studied atEα= 10 MeV andEd= 4.7 MeV using particle-gamma and gamma-gamma coincidence technique. Energies and gamma radiation branching ratios of levels in25Mg up to 6 MeV have been obtained.
Cusp Catastrophes and Phase Transitions in Dense Nuclear Matter and Finite Nuclei
Authors: Carl-G Källman
Published: January 2007

Thom's theory for elementary catastrophes is outlined. Some physical instabilities are discussed and it is suggested that the back-bending of the moment of inertia of elements in the rare earth region can be described within this model.
Nuclear Deformations, Level Assignments and Static Nuclear Moments of Isotopes in the Region72Hf-77Ir
Authors: C Ekström  , H Rubinsztein  , P Möller
Published: January 2007

A comparison is made between experimental and theoretical level assignments and static electromagnetic moments of nuclei in the region72Hf-77Ir. The theoretical calculations are based on the modified oscillator model. Equilibrium deformation values, ϵ and ϵ4, are determined for doubly-even and odd-mass nuclei from the minima in the potential energy surfaces. The influence of the different parameters entering the expressions for the magnetic dipole moment is analysed. The electric quadrupole and hexadecapole moments are calculated on the assumption that the nucleus is a homogeneously charged body with a sharp surface and a shape corresponding to that of an equipotential surface. In some selected cases, the electric multipole moments are evaluated by use of the single-particle wave functions.
Beam-Foil Studies of 720 keV Aluminum Ions
Authors: K Weckström  , K-E Nystén
Published: January 2007

The beam-foil method has been used for spectral studies of aluminum in the wavelength region 1 800-7 000 Å. Most of the lines were from Al III and Al IV, and several hydrogenic transitions were identified in Al IV-Al VI. Mean lives of 10 excited states in Al III are presented. Correction for analyzed main cascades has been applied when possible. In general, good agreement was found with earlier experimental results and theoretical estimates. The cascade correction method was also tested with simulated decay curves and proved to give a better estimate of the lifetime than the multiexponential fit.
4p-5s Transitions in Y VII, VIII, Zr VIII, IX, Nb IX, X and Mo X, XI
Authors: K Rahimullah  , M S Z Chaghtai  , S Khatoon
Published: January 2007

The spectra of Y VII, VIII, Zr VIII, IX, Nb X and Mo X, XI are studied for the first time and our 1971 analysis of Nb IX is improved. By analyses of the transitions 4s
24pk
-4s
24p

k-15s all the levels of the configurations 4p
3, 4p
25s, 4p
2 and 4p5s are established in the spectra concerned.
Effect of the Spatial Resolution Function of the Spectrometer on the Analysis of Multi-exponential Beam-foil Decay Curves
Authors: Y Baudinet-Robinet  , H P Garnir  , P D Dumont  , A E Livingston
Published: January 2007

The effect of the spatial resolution function of the spectrometer on beamfoil lifetime measurements is studied. Intensity curves obtained by convolution of the measured spatial resolution function and a sum of exponentials are compared with measured decay curves. Optimum spatial resolution functions are discussed and results of the analysis of decay curves obtained using different beam lengths viewed by the spectrometer are given, for two transitions presenting strong cascading: 3s3d3D-3s4f3F0in SV (568 Å) and 3d2D-4f2F0in S VI (465 Å).
Valence Electron Spectra of Benzene and the Hexafluorides of Sulphur, Molybdenum, Tungsten and Uranium. An Application of Multichannel Detector Technique to UV-Valence Electron Spectroscopy
Authors: L Karlsson  , L Mattsson  , R Jadrny  , T Bergmark  , K Siegbahn
Published: January 2007

HeI induced valence electron spectra of benzene and the hexafluorides of sulphur, molybdenum, tungsten and uranium are presented together with a HeII spectrum of sulphur hexafluoride. Vibrational band structure has been resolved in the spectra of all molecules and the energies of these bands are reported. A description is also given of the multichannel detector system which has facilitated the recordings of these spectra.
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.
Molecular Motion of Polyethylene Oxide in Dilute Aqueous and Non-aqueous Solutions
Authors: U Dahlborg  , E Braun
Published: January 2007

Neutron scattering measurements on dilute solutions, aqueous and nonaqueous, of polyethylene oxide are reported. No interaction of a hydrophobic or hydrophilic nature is detected in water. The spectra from polyethylene oxide molecules over almost the whole momentum transfer region can be explained in terms of Langevin diffusion models both for the translational and the rotational motion. At small momentum transfers (x < 0.5 A-1) another molecular motion involving large amplitudes and small characteristic times should be included. This unknown motion may involve conformational changes of the molecule but also spontaneous fluctuations of its long axis.
An AC Resistance Bridge for Low Resistance Measurements
Authors: Uno Gäfvert
Published: January 2007

A low frequency AC resistance bridge, suitable for high resolution measurements on small resistances, is described. A precision of 0.01% can be obtained down to the milliohm range with a sample current of 10 mA. A special current comparator is used to automatically keep a constant ratio between the sample current and the current through the balancing decade resistor. The sample current may be up to ten thousand times larger than the current through the decade resistor. The two currents are kept in phase via optical coupling.
The g-Factor of the First Excited State in 95Mo
Authors: K Johansson  , E Karlsson  , L O Norlin
Published: January 2007

The g-factor of the first 3/2+ excited level in 95Mo was determined by perturbing the angular correlation of the 582-204 keV and the 835-204 keV γγ-cascades in three different external fields. A cubic metal lattice (Ag-95Tc) was used in the g-factor experiment as there are no interfering perturbation effects due to quadrupole interactions and no paramagnetic correction of the applied magnetic field in such sources. The result for the g-factor is g = -0.246±0.010.
Energy Levels in 240, 242, 244Am Studied by Deuteron-induced Neutron Transfer
Authors: T Grotdal  , L Guldberg  , K Nybø  , T F Thorsteinsen
Published: January 2007

Targets of 241Am and 243Am were bombarded with 12 MeV deuterons in order to study energy levels in 240,242,244Am. The scattered particles were analysed in a broad range magnetic spectrograph. The measured ground state Q-values are -(0.388±0.015) MeV for the 241Am(d,t)240Am-reaction, -(0.111±0.015) MeV for the 243Am(d,t)242Am reaction and (3.308±0.015) MeV for the 241Am(d,p)242Am reaction. The neutron orbitals 631↓ and 501↑ are observed in 240,242Am. The 620↑ orbital is observed in 242,244Am, and the 622↑ orbital is observed in 240,242,244Am. The neutron orbitals are assumed to be coupled to the 523↓ proton orbital.
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 form

whereI0is 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.
Structure hyperfine de la transition 2S1/2-2P1/2 de Hg II (γ=194,2 nm)
Authors: Y Guern  , A Bideau-Méhu  , R Abjean  , A Johannin-Gilles
Published: January 2007

The hyperfine structure of the 194.2 nm line of Hg II has been studied by Fabry-Pérot interferometry. The A-factors for the odd isotopes have been determined for the levels 2
S
1/2 and 2
P
1/2 and the shifts for the different isotopes in the natural mercury line have been measured.
Etude des distributions des états de charge à l'équilibre d'ions énergétiques de bore dans le carbone et observation de niveaux d'énergie doublement excités du B III
Authors: K X To  , R Drouin
Published: January 2007

The equilibrium charge distributions for boron ions after interacting with a thin carbon foil has been measured for incident energies between 2 and 7 MeV. An empirical formula derived from an original proposal of Nikolaev and Dmitriev [1] has been used to predict our measurements and those of other authors. Using the beam-foil method, the energy of 3 MeV has been selected to continue our studies of doubly excited states in B III. Eight new transitions have been observed in the spectral region of 300 and 1 400 ångströms.
The Transitions 4p-5s in Y VI, Zr VII, Nb VIII and Mo IX
Authors: M S Z Chaghtai  , K Rahimullah  , S Khatoon
Published: January 2007

With the help of the spectra recorded in the Physics Department of Lund University, Y VI, Zr VII, Nb VIII and Mo IX are freshly analysed. The five 4s24p4ground levels and the ten 4s24p35slevels of previous analyses are confirmed in the first three spectra, except for revising in Y VI the 4p41S0and 4p35s(4S3/2)2levels and interchanging 5s(2D3/2)1with 5s(2D3/2)2. All level values are improved due to our new measurements. A new analysis of Mo IX establishing all the 4p4and 4p35slevels is being reported.
Extension of the Analysis of Quadruply Ionized Silicon (Si V)
Authors: Wan-Ü Lydia Brillet  , Marie-Christine Artru
Published: January 2007

The observations of the Si V spectrum has been extended in the wavelength range 460-3 604 Å; about 120 new lines have been observed and classified. All the levels belonging to the 2p54p, 4d, 4f, 5fand 5gconfigurations are located. Results of parametric calculations of these configurations are given. The first ionization limit has been determined at 1 345 070 cm-1by means of the polarization formula.
Predissociation Rates and Perturbations of the A, B, B', C, D and F States in NO Studied Using Time Resolved Spectroscopy
Authors: J Brzozowski  , P Erman  , M Lyyra
Published: January 2007

Radiative lifetimes of theA2Σ+,B2Π,B'2Δ,C2Π,D2Σ+andF2Δ electronic states in NO have been measured at high spectral resolution using the High Frequency Deflection technique. Particular attention has been paid to levels in the vicinity of or above the first dissociation limit in order to search for predissociation effects. The well-known effect in theCstate is confirmed, while new predissociations of theAandDstates and their rates are established. An anomaly in the lifetime series (B', v= 0-5) atv= 4 is explained in terms of theB'(v= 4) ∼F(v= 1) configuration interaction. The variation in theA-Xtransition moment has been measured and found to be substantially different from earlier estimates.
The Low Lying Electronic States of SiO
Authors: R W Field  , A Lagerqvist  , I Renhorn
Published: January 2007

Perturbations in theA1Π state of the isotopic28Si16O and28Si18O molecules are analyzed. The perturbing states,d3Δr,e3Σ-,C1Σ-, andD1Δ, are identified and vibrationally assigned. Two independent methods of vibrationally numbering the perturbers, employing isotope shifts and vibrational variation of perturbation matrix elements, respectively, are described in detail and shown to be in complete agreement. Molecular constants for the eight lowest energy electronic states of SiO are presented. Semiempirical and isovalent relationships between spin-orbit and spin-spin constants are discussed.
Influence of a Circularly Polarized Electromagnetic Wave on a Magnetized Plasma
Authors: L Stenflo
Published: January 2007

A dispersion relation is derived for a magnetized plasma in which a large amplitude circularly polarized wave propagates along the external magnetic field. It is shown that new modes, which appear due to relativistic effects, can be unstable.
Parametric Wave Interactions in Random Media
Authors: D Anderson  , A Bondeson
Published: January 2007

An investigation is made of parametric wave interaction processes in media, where characteristic parameters contain small statistically varying deviations from uniformity. Effective growth-rates are evaluated for various statistical limits including also the case of a slowly varying deterministic inhomogeneity.
Software package for automatic microarray image analysis (MAIA)
Authors: Novikov Eugene , Barillot Emmanuel
Published: January 2007

Summary: 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

Motivation: 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 >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.edu

Supplementary 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

Summary: 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.ca

Supplementary 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

Summary: 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.uk

Supplementary 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

Helical 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

Motivation: 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

Summary: 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

Summary: 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.nl

Supplementary 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

Motivation: 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

Motivation: 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/~bmb4sjc

Contact:  r.m.jackson@leeds.ac.uk

Supplementary 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

Motivation: 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.cn

Contact:  mzhang@cshl.edu  mli@uwaterloo.ca

Supplementary 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

Motivation: 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
Quick calculation for sample size while controlling false discovery rate with application to microarray analysis
Authors: Liu Peng , Hwang J. T. Gene
Published: January 2007

Motivation: Sample size calculation is important in experimental design and is even more so in microarray or proteomic experiments since only a few repetitions can be afforded. In the multiple testing problems involving these experiments, it is more powerful and more reasonable to control false discovery rate (FDR) or positive FDR (pFDR) instead of type I error, e.g. family-wise error rate (FWER). When controlling FDR, the traditional approach of estimating sample size by controlling type I error is no longer applicable.

Results: Our proposed method applies to controlling FDR. The sample size calculation is straightforward and requires minimal computation, as illustrated with two sample t-tests and F-tests. Based on simulation with the resultant sample size, the power is shown to be achievable by the q-value procedure.

Availability: A Matlab code implementing the described methods is available upon request.

Contact:  pliu@iastate.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences
Authors: Ye Kai , Kosters Walter A. , IJzerman Adriaan P.
Published: January 2007

Motivation: Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets.

Results: In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets.

Availability: The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/

Contact:  k.ye@lacdr.leidenuniv.nl
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors
Authors: Yoneya Takashi , Mamitsuka Hiroshi
Published: January 2007

Motivation: Time series experiments of cDNA microarrays have been commonly used in various biological studies and conducted under a lot of experimental factors. A popular approach of time series microarray analysis is to compare one gene with another in their expression profiles, and clustering expression sequences is a typical example. On the other hand, a practically important issue in gene expression is to identify the general timing difference that is caused by experimental factors. This type of difference can be extracted by comparing a set of time series expression profiles under a factor with those under another factor, and so it would be difficult to tackle this issue by using only a current approach for time series microarray analysis.

Results: We have developed a systematic method to capture the timing difference in gene expression under different experimental factors, based on hidden Markov models. Our model outputs a real-valued vector at each state and has a unique state transition diagram. The parameters of our model are trained from a given set of pairwise (generally multiplewise) expression sequences. We evaluated our model using synthetic as well as real microarray datasets. The results of our experiment indicate that our method worked favourably to identify the timing ordering under different experimental factors, such as that gene expression under heat shock tended to start earlier than that under oxidative stress.

Contact:  t-yoneya@kirin.co.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB
Authors: Schmidt Henning
Published: January 2007

Summary: We present the SBaddon package as an extension to the Systems Biology Toolbox for MATLAB (SBtoolbox). The goal of this extension is to provide the users of the SBtoolbox with important functionality that is needed for parameter estimation applications. While simulation in the SBtoolbox relies on the MATLAB ODE solvers, the SBaddon package provides considerably increased simulation performance through automatic generation of compiled simulation functions. Furthermore, the package contains improved optimization algorithms, forward parameter sensitivity analysis and basic numeric parameter identifiability analysis.

Availability: The SBaddon package is open source and freely available for non-commercial use. Commercial use of SBaddon is only possible through a specific licensing agreement (contact sbaddon@sbtoolbox.org). SBaddon can be obtained from http://www.sbtoolbox.org/SBaddon. The website also contains extensive documentation, and examples.

Contact:  henning@fcc.chalmers.se
A 3D pattern matching algorithm for DNA sequences
Authors: Hérisson Joan , Payen Guillaume , Gherbi Rachid
Published: January 2007

Motivation: Biologists usually work with textual DNA sequences (succession of A, C, G and T). This representation allows biologists to study the syntax and other linguistic properties of DNA sequences. Nevertheless, such a linear coding offers only a local and a one-dimensional vision of the molecule. The 3D structure of DNA is known to be very important in many essential biological mechanisms. By using 3D conformation models, one is able to construct a 3D trajectory of a naked DNA molecule. From the various studies that we performed, it turned out that two very different textual DNA sequences could have similar 3D structures.

Results: In this article, we address a new research work on 3D pattern matching for DNA sequences. The aim of this work is to enhance conventional pattern matching analyses with 3D-augmented criteria. We have developed an algorithm, based on 3D trajectories, which compares angles formed by these trajectories and thus quantifies the difference between two 3D DNA sequences. This analysis performs from a global scale to al local one.

Availability: Available on request from the authors.

Contact:  herisson@epigenomique.genopole.fr