Efficient -tensor determination and NH assignment of paramagnetic proteins

Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D N-15-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly N-15-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.

Orbital currents and charge density waves in a generalized Hubbard ladder

We study a generalized Hubbard model on the two-leg ladder at zero temperature, focusing on a parameter region with staggered flux (SF)/d-density wave (DDW) order. To guide our numerical calculations, we first investigate the location of a SF/DDW phase in the phase diagram of the half-filled weakly interacting ladder using a perturbative renormalization group (RG) and bosonization approach. For hole doping 6 away from half-filling, finite-system density-matrix renormalizationgroup (DMRG) calculations are used to study ladders with up to 200 rungs for intermediate-strength interactions. In the doped SF/DDW phase, the staggered rung current and the rung electron density both show periodic spatial oscillations, with characteristic wavelengths 2/delta and 1/delta, respectively, corresponding to ordering wavevectors 2k(F) and 4k(F) for the currents and densities, where 2k(F) = pi(1 - delta). The density minima are located at the anti-phase domain walls of the staggered current. For sufficiently large dopings, SF/DDW order is suppressed. The rung density modulation also exists in neighboring phases where currents decay exponentially. We show that most of the DMRG results can be qualitatively understood from weak-coupling RG/bosonization arguments. However, while these arguments seem to suggest a crossover from non-decaying correlations to power-law decay at a length scale of order 1/delta, the DMRG results are consistent with a true long-range order scenario for the currents and densities. (c) 2005 Elsevier Inc. All rights reserved.

Segmenting eukaryotic genomes with the generalized Gibbs sampler

Eukaryotic genomes display segmental patterns of variation in various properties, including GC content and degree of evolutionary conservation. DNA segmentation algorithms are aimed at identifying statistically significant boundaries between such segments. Such algorithms may provide a means of discovering new classes of functional elements in eukaryotic genomes. This paper presents a model and an algorithm for Bayesian DNA segmentation and considers the feasibility of using it to segment whole eukaryotic genomes. The algorithm is tested on a range of simulated and real DNA sequences, and the following conclusions are drawn. Firstly, the algorithm correctly identifies non-segmented sequence, and can thus be used to reject the null hypothesis of uniformity in the property of interest. Secondly, estimates of the number and locations of change-points produced by the algorithm are robust to variations in algorithm parameters and initial starting conditions and correspond to real features in the data. Thirdly, the algorithm is successfully used to segment human chromosome 1 according to GC content, thus demonstrating the feasibility of Bayesian segmentation of eukaryotic genomes. The software described in this paper is available from the author's website (www.uq.edu.au/similar to uqjkeith/) or upon request to the author.

Signatures for generalized macroscopic superpositions

We develop criteria sufficient to enable detection of macroscopic coherence where there are not just two macroscopically distinct outcomes for a pointer measurement, but rather a spread of outcomes over a macroscopic range. The criteria provide a means to distinguish a macroscopic quantum description from a microscopic one based on mixtures of microscopic superpositions of pointer-measurement eigenstates. The criteria are applied to Gaussian-squeezed and spin-entangled states.

Validation of a generalized transfer function to noninvasively derive central blood pressure during exercise

Exercise brachial blood pressure ( BP) predicts mortality, but because of wave reflection, central ( ascending aortic) pressure differs from brachial pressure. Exercise central BP may be clinically important, and a noninvasive means to derive it would be useful. The purpose of this study was to test the validity of a noninvasive technique to derive exercise central BP. Ascending aortic pressure waveforms were recorded using a micromanometer-tipped 6F Millar catheter in 30 patients (56 +/- 9 years; 21 men) undergoing diagnostic coronary angiography. Simultaneous recordings of the derived central pressure waveform were acquired using servocontrolled radial tonometry at rest and during supine cycling. Pulse wave analysis of the direct and derived pressure signals was performed offline (SphygmoCor 7.01). From rest to exercise, mean arterial pressure and heart rate were increased by 20 +/- 10 mm Hg and 15 +/- 7 bpm, respectively, and central systolic BP ranged from 77 to 229 mm Hg. There was good agreement and high correlation between invasive and noninvasive techniques with a mean difference (+/- SD) for central systolic BP of -1.3 +/- 3.2 mm Hg at rest and -4.7 +/- 3.3 mm Hg at peak exercise ( for both r=0.995; P < 0.001). Conversely, systolic BP was significantly higher peripherally than centrally at rest (155 +/- 33 versus 138 +/- 32mm Hg; mean difference, -16.3 +/- 9.4mm Hg) and during exercise (180 +/- 34 versus 164 +/- 33 mm Hg; mean difference, -15.5 +/- 10.4 mm Hg; for both P < 0.001). True myocardial afterload is not reliably estimated by peripheral systolic BP. Radial tonometry and pulse wave analysis is an accurate technique for the noninvasive determination of central BP at rest and during exercise.

Generalized Perk-Schultz models: solutions of the Yang-Baxter equation associated with quantized orthosymplectic superalgebras

The Perk-Schultz model may be expressed in terms of the solution of the Yang-Baxter equation associated with the fundamental representation of the untwisted affine extension of the general linear quantum superalgebra U-q (gl(m/n)], with a multiparametric coproduct action as given by Reshetikhin. Here, we present analogous explicit expressions for solutions of the Yang-Baxter equation associated with the fundamental representations of the twisted and untwisted affine extensions of the orthosymplectic quantum superalgebras U-q[osp(m/n)]. In this manner, we obtain generalizations of the Perk-Schultz model.

The moving targets algorithm for difficult temporal credit assignment problems

The 'moving targets' algorithm for training recurrent networks is reviewed and applied to a task which demonstrates the ability of this algorithm to use distant contextual information. Some practical difficulties are discussed, especially with regard to the minimization process. Results on performance and computational requirements of several different 2nd-order minimization algorithms are presented for moving target problems.