Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

QUANTIFICATION AND PARTIAL CHARACTERIZATION OF REGULATORY PEPTIDES IN THE LIVER FLUKE, FASCIOLA-HEPATICA, FROM DIFFERENT MAMMALIAN HOSTS

1. Extracts of the liver fluke, Fasciola hepatica from three different hosts (cow, sheep, rat) have been subjected to radioimmunoassay using antisera to 6 mammalian regulatory peptides.

A Low Complexity Real-time MIMO-Preprocessing For Fixed Complexity Sphere Decoder

Modern Multiple-Input Multiple-Output (MIMO) communication systems place huge demands on embedded processing resources in terms of throughput, latency and resource utilization. State-of-the-art MIMO detector algorithms, such as Fixed-Complexity Sphere Decoding (FSD), rely on efficient channel preprocessing involving numerous calculations of the pseudo-inverse of the channel matrix by QR Decomposition (QRD) and ordering. These highly complicated operations can quickly become the critical prerequisite for real-time MIMO detection, exaggerated as the number of antennas in a MIMO detector increases. This paper describes a sorted QR decomposition (SQRD) algorithm extended for FSD, which significantly reduces the complexity and latency
of this preprocessing step and increases the throughput of MIMO detection. It merges the calculations of the QRD and ordering operations to avoid multiple iterations of QRD. Specifically, it shows that SQRD reduces the computational complexity by over 60-70% when compared to conventional
MIMO preprocessing algorithms. In 4x4 to 7x7 MIMO cases, the approach suffers merely 0.16-0.2 dB reduction in Bit Error Rate (BER) performance.

FASCIOLA-HEPATICA - LOCALIZATION AND PARTIAL CHARACTERIZATION OF TUBULIN

The localisation and distribution of the cytoskeletal protein tubulin in the adult liver fluke Fasciola hepatica have been determined by an indirect immunofluorescence technique using a monoclonal antibody raised against beta-tubulin. Tubulin was demonstrated in the tegumental syncytium and in the tegumental cell bodies and their cytoplasmic connections with the surface syncytium. Immunostaining was also evident in the nerve fibres innervating sensory receptors in the tegument, in the nerve plexus innervating the sub-tegumental musculature and in the cytoplasmic extensions of the nurse cells within the vitelline follicle. Immunoblotting of whole fluke fractions produced a single band corresponding to a molecule of approximately 54 kDa in size. This figure corresponds with previous data obtained on tubulin from other helminth and eukaryotic sources.

ISOLATION AND PARTIAL SEQUENCING OF A PANCREATIC POLYPEPTIDE-LIKE NEUROPEPTIDE FROM THE LIVER FLUKE, FASCIOLA-HEPATICA

1. A pancreatic polypeptide (PP)-immunoreactive neuropeptide has been isolated and partially sequenced from the liver fluke, Fasciola hepatica.

Partial and total multiphoton detachment rates for H- in a perturbative B-spline-based approach

An ab initio approach has been applied to study multiphoton detachment rates for the negative hydrogen ion in the lowest nonvanishing order of perturbation theory. The approach is based on the use of B splines allowing an accurate treatment of the electronic repulsion. Total detachment rates have been determined for two- to six-photon processes as well as partial rates for detachment into the different final symmetries. It is shown that B-spline expansions can yield accurate continuum and bound-state wave functions in a very simple manner. The calculated total rates for two- and three-photon detachment are in good agreement with other perturbative calculations. For more than three-photon detachment little information has been available before now. While the total cross sections show little structure, a fair amount of structure is predicted in the partial cross sections. In the two-photon process, it is shown that the detached electrons mainly have s character. For four- and six-photon processes, the contribution from the d channel is the most important. For three- and five-photon processes p electrons dominate the electron emission spectrum. Detachment rates for s and p electrons show minima as a function of photon energy. © 1994 The American Physical Society.

The agonism and synergistic potentiation of weak partial agonists by triethylamine in alpha(1)-adrenergic receptor activation: Evidence for a salt bridge as the initiating process

alpha(1)-adrenergic receptor (AR) activation is thought to be initiated by disruption of a constraining interhelical salt bridge (Porter et al., 1996). Disruption of this salt bridge is achieved through a competition for the aspartic acid residue in transmembrane domain three by the protonated amine of the endogenous ligand norepinephrine and a lysine residue in transmembrane domain seven. To further test this hypothesis, we investigated the possibility that a simple amine could mimic an important functional group of the endogenous ligand and break this alpha(1)-AR ionic constraint leading to agonism. Triethylamine (TEA) was able to generate concentration-dependent increases of soluble inositol phosphates in COS-1 cells transiently transfected with the hamster alpha(1b)-AR and in Rat-1 fibroblasts stably transfected with the human alpha(1a)-AR subtype. TEA was also able to synergistically potentiate the second messenger production by weak partial alpha(1)-AR agonists and this effect was fully inhibited by the alpha(1)-AR antagonist prazosin. However, this synergistic potentiation was not observed for full alpha(1)-AR agonists. Instead, TEA caused a parallel rightward shift of the dose-response curve, consistent with the properties of competitive antagonism. TEA specifically bound to a single population of alpha(1)-ARs with a K-i of 28.7 +/- 4.7 mM. In addition, the site of binding by TEA to the alpha(1)-AR is at the conserved aspartic acid residue in transmembrane domain three, which is part of the constraining salt bridge. These results indicate a direct interaction of TEA in the receptor agonist binding pocket that leads to a disruption of the constraining salt bridge, thereby initiating alpha(1)-AR activation.

Modelling and fixed bed column adsorption of Cr(VI) onto orthophosphoric acid-activated lignin

The advantage of using an available and abundant residual biomass, such as lignin, as a raw material for activated carbons is that it provides additional economical interest to the technical studies. In the current investigation, a more complete understanding of adsorption of Cr(VI) from aqueous systems onto H PO -acid activated lignin has been achieved via microcolumns, which were operated under various process conditions. The practice of using microcolumn is appropriate for defining the adsorption parameters and for screening a large number of potential adsorbents. The effects of solution pH (2-8), initial metal ion concentration (0.483-1.981 mmol·L ), flow rate (1.0-3.1 cm ·min ), ionic strength (0.01-0.30 mmol·L ) and adsorbent mass (0.11-0.465 g) on Cr(VI) adsorption were studied by assessing the microcolumn breakthrough curve. The microcolumn data were fitted by the Thomas model, the modified Dose model and the BDST model. As expected, the adsorption capacity increased with initial Cr(VI) concentration. High linear flow rates, pH values and ionic strength led to early breakthrough of Cr(VI). The model constants obtained in this study can be used for the design of pilot scale adsorption process. © 2012 Chemical Industry and Engineering Society of China (CIESC) and Chemical Industry Press (CIP).