Stability of functions in Boolean models of gene regulatory networks

Boolean networks are used to model large nonlinear systems such as gene regulatory networks. We will present results that can be used to understand how the choice of functions affects the network dynamics. The so called bias-map and its fixed points depict much of the function's dynamical role in the network. We define the concept of stabilizing functions and show that many Post and canalizing functions are also stabilizing functions. Boolean networks constructed using the same type of stabilizing functions are always stable regardless of the average in-degree of network functions. We derive the number of all stabilizing functions and find it to be much larger than the number of Post and canalizing functions. We also discuss the implementation of functions and apply the presented results to biological data that give an approximation of the distribution of regulatory functions in eucaryotic cells. We find that the obtained theoretical results on the number of active genes are biologically plausible. Finally, based on the presented results, we discuss why canalizing and Post regulatory functions seem to be common in cells.     

Projection screen or video goggles as stimulus modality in functional magnetic resonance imaging

The purpose of this study was to investigate the reliability of functional magnetic resonance imaging (fMRI) by using either a projection screen or video goggles as stimulus modality. A sequence of visual stimuli were presented to the same subject at different occasions. The sequence was optimized with a genetic algorithm. In five sessions the stimuli were presented using a projection screen viewed through a mirror in the head coil and in five sessions using video goggles. Failure to detect visual activation in the medial left hemisphere was observed in sessions using the projection screen as stimulus modality. Decreased thresholds for P values and cluster size resulted in activation outside the occipital lobe and did not significantly increase activated areas in this region. Results in this study indicate that presentation of fMRI tasks with visual routes is more reliable with direct input through video goggles than with the conventional use of projection screens. Failure to detect crucial visual areas has severe consequences for tumor surgery in the visual cortex. Inferior visual impression might also have negative consequences for cognitive tests with high demand on attention and perception.     

Retrieval of transverse relaxation time distribution from spin-echo data by recurrent neural network

Inversion of transverse relaxation time decay curve from spin-echo experiments was carried out using Hopfield neural network, to obtain the transverse relaxation time distribution. The performance of this approach was tested against simulated and experimental data. The initial guess, necessary for the integration procedure, was established as the analytical Laplace inversion. Together with errors in the simulated data, inversion was also carried out with errors in this initial guess. The probability density function, calculated by the neural network, is used in multiple sclerosis diagnostics.     

Isospin breaking in $K\to3\pi$ decays II: radiative corrections

The five different CP conserving amplitudes for the decays are calculated using Chiral Perturbation Theory. The calculation is made to next-to-leading order and includes full isospin breaking. The squared amplitudes are compared with the corresponding ones in the isospin limit to estimate the size of the isospin breaking effects. In this paper we add the radiative corrections to the earlier calculated m _u -m _d and local electromagnetic effects. We find corrections of order 5-10 percent. Received: 8 November 2004, Published online: 18 January 2005 PACS: 13.20.Eb; 12.39.Fe; 14.40.Aq; 11.30.Rd     

Transverse-momentum-ordered showers and interleaved multiple interactions

We propose a sophisticated framework for high-energy hadronic collisions, wherein different QCD physics processes are interleaved in a common sequence of falling transverse-momentum values. Thereby phase-space competition is introduced between multiple parton-parton interactions and initial-state radiation. As a first step we develop new transverse-momentum-ordered showers for initial- and final-state radiation, which should be of use also beyond the scope of the current article. These showers are then applied in the context of multiple interactions, and a few tests of the new model are presented. The article concludes with an outlook on further aspects, such as the possibility of a shower branching giving partons participating in two different interactions.Received: 26 August 2004, Revised: 14 October 2004, Published online: 11 January 2005     

Enantioselectivity in Ni(II) Schiff-base complexes derived from amino-acids and (S)-o-N-(N-benzylprolyl)aminobenzophenone: molecular structure of several chiral Ni(II) Schiff-base complexes, circular dichroism and molecular mechanics studies

Several Ni(II) complexes derived from (S)-o-N-(N-benzylprolyl)aminobenzophenone ((S)-BBP) and amino acids of general formula [Ni((S)-BBP-L-(or D-)-aa)] were prepared. The crystal and molecular structures of [Ni((S)-BBP-Gly)], [Ni((S)-BBP-L-Ser)] and [Ni((S)-BBP-L-aaIm)](aaIm =L-2-amino-3-(imidazol-1-yl)propanoate were determined by X-ray diffraction analysis. In the three complexes the nickel atoms display a square-planar coordination and the overall structure around the metal indicates that the entire Schiff-base ligands form quite rigid frameworks. Molecular mechanics calculations were carried out for complexes [Ni((S)-BBP-Gly)], [Ni((S)-BBP-Ser)] and [Ni((S)-BBP-aaIm)] containing either the L- or D-amino acid forms, and the factors controlling the stereoselectivity are discussed. Several other [Ni((S)-BBP-L-aa)] complexes are also prepared and their circular dichroism spectra in solution and of the solids dispersed in KBr disks are measured and discussed. In agreement with other studies in solution with similar [Ni((S)-BBP-aa)] complexes, the Cotton effects for the bands with lambda(max) at 520--530 nm are positive when the amino acids have the L-configuration at the alpha-carbon. The same is observed in this work for the solid-state CD spectra of all compounds.     

Graphical analysis of electrochemical impedance spectroscopy of two consecutive irreversible electron transfers. 2. Zinc anodic dissolution in acid media

The graphical analysis of the impedance plots is used in the study of the electrodic systems that take place through two consecutive single electron transfers. The zinc anodic dissolution is studied by using this procedure. The characteristic points easily allow us to explain and to simulate the impedance behavior of this electrodic system according to the steady-state potential and the roughness of the working electrode. The direct procedure for parametrical identification from the graphical analysis allows us to reduce the time needed for an impedance experiment. This graphical analysis is suggested for studying thin coated galvanized steels.     

Selective synthesis of the C3v isomer of C60h18

[chemical structure: see text]. C60H18 has been produced by hydrogenation of C60 at 100 bar H2 pressure and 673 K for 10 h. We have investigated the crude material without any purification by use of 1H NMR, 13C NMR, and IR spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry. We show that the crude material consists of 95% of the C3v isomer of C60H18.     

Measurement of time-dependent CP-violating asymmetries in B0 --> K(s)0K(s)0K(s)0 decay

We present a measurement of CP-violation parameters in the B0 --> K(s)0K(s)0K(s)0 decay based on a sample of 275 x 10(6) BB pairs collected at the upsilon(4S) resonance with the Belle detector at the KEKB energy-asymmetric e+e- collider. One neutral B meson is fully reconstructed in the decay B0 --> K(s)0K(s)0K(s)0, and the flavor of the accompanying B meson is identified from its decay products. CP-violation parameters are obtained from the asymmetry in the distributions of the proper-time interval between the two B decays: S = +1.26 +/- 0.68(stat) +/- 0.20(syst) and [symbol: see text] = +0.54 +/- 0.34(stat) +/- 0.09(syst).     

Quantitative analysis of WC grain shape in sintered WC-Co cemented carbides

The morphology of WC grains is examined by ab initio calculations, and by transmission electron microscopy in a WC-Co cemented carbide. Two compositions are studied to determine the effect of carbon chemical potential on the shape development. The WC grains are found to be truncated triangles, and the grain morphology is adequately reproduced by the ab initio calculations. The energy difference between the two types of grain facets is shown to be due to the formation of stronger bonds with more covalent character between low coordinated W and Co atoms at one type of facet.