Expressed sequence tag analysis of genes expressed during development of the tropical abalone Haliotis asinina

The tropical abalone. Haliotis asinina. is,in ideal species to investigate the molecular mechanisms that control development. growth, reproduction and shell formation in all cultured haliotids. Here we describe the analysis of 232 expressed sequence tags (EST) obtained front a developmental H. asinina cDNA library intended for future microarray studies. From this data set we identified 183 unique gene Clusters. Of these, 90 clusters showed significant homology with sequences lodged in GenBank, ranging in function from general housekeeping to signal transduction, gene regulation and cell-cell communication. Seventy-one clusters possessed completely novel ORFs greater than 50 codons in length, highlighting the paucity of sequence data from molluscs and other lophotrochozoans. This study of developmental gene expression in H. asinina provides the foundation for further detailed analyses of abalone growth, development and reproduction.

Reconstruction and in silico analysis of the MAPK signaling pathways in the human blood fluke, Schistosoma japonicum

At present, little is known about signal transduction mechanisms in schistosomes, which cause the disease of schistosomiasis. The mitogen-activated protein kinase (MAPK) signaling pathways, which are evolutionarily conserved from yeast to Homo sapiens, play key roles in multiple cellular processes. Here, we reconstructed the hypothetical MAPK signaling pathways in Schistosoma japonicum and compared the schistosome pathways with those of model eukaryote species. We identified 60 homologous components in the S. japoncium MAPK signaling pathways. Among these, 27 were predicted to be full-length sequences. Phylogenetic analysis of these proteins confirmed the evolutionary conservation of the MAPK signaling pathways. Remarkably, we identified S. japonicum homologues of GTP-binding protein beta and alpha-I subunits in the yeast mating pathway, which might be involved in the regulation of different life stages and female sexual maturation processes as well in schistosomes. In addition, several pathway member genes, including ERK, JNK, Sja-DSP, MRAS and RAS, were determined through quantitative PCR analysis to be expressed in a stage-specific manner, with ERK, JNK and their inhibitor Sja-DSP markedly upregulated in adult female schistosomes. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Seizure detection algorithm for neonates based on wave-sequence analysis

Objective: The description and evaluation of the performance of a new real-time seizure detection algorithm in the newborn infant. Methods: The algorithm includes parallel fragmentation of EEG signal into waves; wave-feature extraction and averaging; elementary, preliminary and final detection. The algorithm detects EEG waves with heightened regularity, using wave intervals, amplitudes and shapes. The performance of the algorithm was assessed with the use of event-based and liberal and conservative time-based approaches and compared with the performance of Gotman's and Liu's algorithms. Results: The algorithm was assessed on multi-channel EEG records of 55 neonates including 17 with seizures. The algorithm showed sensitivities ranging 83-95% with positive predictive values (PPV) 48-77%. There were 2.0 false positive detections per hour. In comparison, Gotman's algorithm (with 30 s gap-closing procedure) displayed sensitivities of 45-88% and PPV 29-56%; with 7.4 false positives per hour and Liu's algorithm displayed sensitivities of 96-99%, and PPV 10-25%; with 15.7 false positives per hour. Conclusions: The wave-sequence analysis based algorithm displayed higher sensitivity, higher PPV and a substantially lower level of false positives than two previously published algorithms. Significance: The proposed algorithm provides a basis for major improvements in neonatal seizure detection and monitoring. Published by Elsevier Ireland Ltd. on behalf of International Federation of Clinical Neurophysiology.

Branching genes are conserved across species. Genes controlling a novel signal in pea are coregulated by other long-distance signals

Physiological and genetic studies with the ramosus (rms) mutants in garden pea (Pisum sativum) and more axillary shoots (max) mutants in Arabidopsis (Arabidopsis thaliana) have shown that shoot branching is regulated by a network of long-distance signals. Orthologous genes RMS1 and MAX4 control the synthesis of a novel graft-transmissible branching signal that may be a carotenoid derivative and acts as a branching inhibitor. In this study, we demonstrate further conservation of the branching control system by showing that MAX2 and MAX3 are orthologous to RMS4 and RMS5, respectively. This is consistent with the longstanding hypothesis that branching in pea is regulated by a novel long-distance signal produced by RMS1 and RMS5 and that RMS4 is implicated in the response to this signal. We examine RMS5 expression and show that it is more highly expressed relative to RMS1, but under similar transcriptional regulation as RMS1. Further expression studies support the hypothesis that RMS4 functions in shoot and rootstock and participates in the feedback regulation of RMS1 and RMS5 expression. This feedback involves a second novel long-distance signal that is lacking in rms2 mutants. RMS1 and RMS5 are also independently regulated by indole-3-acetic acid. RMS1, rather than RMS5, appears to be a key regulator of the branching inhibitor. This study presents new interactions between RMS genes and provides further evidence toward the ongoing elucidation of a model of axillary bud outgrowth in pea.

Signal or Noise? Information Theory and the Novel

In the context of a hostile funding environment, universities are increasingly asked to justify their output in narrowly defined economic terms, and this can be difficult in Humanities or Arts faculties where productivity is rarely reducible to a simple financial indicator. This can lead to a number of immediate consequences that I have no need to rehearse here, but can also result in some interesting tensions within the academic community itself. First is that which has become known as the ‘Science Wars’: the increasingly acrimonious exchanges between scientists and scientific academics and cultural critics or theorists about who has the right to describe the world. Much has already been said—and much remains to be said—about this issue, but it is not my intention to discuss it here. Rather, I will look at a second area of contestation: the incorporation of scientific theory into literary or cultural criticism. Much of this work comes from a genuine commitment to interdisciplinarity, and an appreciation of insights that a fresh perspective can bring to a familiar object. However, some can be seen as cynical attempts to lend literary studies the sort of empirical legitimacy of the sciences. In particular, I want to look at a number of critics who have applied information theory to the literary work. In this paper, I will examine several instances of this sort of criticism, and then, through an analysis of a novel by American author Richard Powers, Three Farmers on Their Way to a Dance, show how this sort of criticism merely reduces the meaningful analysis of a complex literary text.

Performance analysis using equivariant kernel density estimator in nonlinear mixture

This paper investigates the performance analysis of separation of mutually independent sources in nonlinear models. The nonlinear mapping constituted by an unsupervised linear mixture is followed by an unknown and invertible nonlinear distortion, are found in many signal processing cases. Generally, blind separation of sources from their nonlinear mixtures is rather difficult. We propose using a kernel density estimator incorporated with equivariant gradient analysis to separate the sources with nonlinear distortion. The kernel density estimator parameters of which are iteratively updated to minimize the output independence expressed as a mutual information criterion. The equivariant gradient algorithm has the form of nonlinear decorrelation to perform the convergence analysis. Experiments are proposed to illustrate these results.

Investigating the performance analysis of EASI algorithm and EKENS algorithm in nonlinear model

This paper investigates the performance of EASI algorithm and the proposed EKENS algorithm for linear and nonlinear mixtures. The proposed EKENS algorithm is based on the modified equivariant algorithm and kernel density estimation. Theory and characteristic of both the algorithms are discussed for blind source separation model. The separation structure of nonlinear mixtures is based on a nonlinear stage followed by a linear stage. Simulations with artificial and natural data demonstrate the feasibility and good performance of the proposed EKENS algorithm.

Signal detection theory in applied tasks: The case of hazard perception in driving

Fuzzy signal detection analysis can be a useful complementary technique to traditional signal detection theory analysis methods, particularly in applied settings. For example, traffic situations are better conceived as being on a continuum from no potential for hazard to high potential, rather than either having potential or not having potential. This study examined the relative contribution of sensitivity and response bias to explaining differences in the hazard perception performance of novices and experienced drivers, and the effect of a training manipulation. Novice drivers and experienced drivers were compared (N = 64). Half the novices received training, while the experienced drivers and half the novices remained untrained. Participants completed a hazard perception test and rated potential for hazard in occluded scenes. The response latency of participants to the hazard perception test replicated previous findings of experienced/novice differences and trained/untrained differences. Fuzzy signal detection analysis of both the hazard perception task and the occluded rating task suggested that response bias may be more central to hazard perception test performance than sensitivity, with trained and experienced drivers responding faster and with a more liberal bias than untrained novices. Implications for driver training and the hazard perception test are discussed.

Adaptive Signal Processing for Power Line Communications

This thesis represents a significant part of the research activity conducted during the PhD program in Information Technologies, supported by Selta S.p.A, Cadeo, Italy, focused on the analysis and design of a Power Line Communications (PLC) system. In recent times the PLC technologies have been considered for integration in Smart Grids architectures, as they are used to exploit the existing power line infrastructure for information transmission purposes on low, medium and high voltage lines. The characterization of a reliable PLC system is a current object of research as well as it is the design of modems for communications over the power lines. In this thesis, the focus is on the analysis of a full-duplex PLC modem for communication over high-voltage lines, and, in particular, on the design of the echo canceller device and innovative channel coding schemes.

The second intracellular loop of the calcitonin gene-related peptide receptor provides molecular determinants for signal transduction and cell surface expression

The calcitonin gene-related peptide (CGRP) receptor is a heterodimer of a family B G-protein-coupled receptor, calcitonin receptor-like receptor (CLR), and the accessory protein receptor activity modifying protein 1. It couples to Gs, but it is not known which intracellular loops mediate this. We have identified the boundaries of this loop based on the relative position and length of the juxtamembrane transmembrane regions 3 and 4. The loop has been analyzed by systematic mutagenesis of all residues to alanine, measuring cAMP accumulation, CGRP affinity, and receptor expression. Unlike rhodopsin, ICL2 of the CGRP receptor plays a part in the conformational switch after agonist interaction. His-216 and Lys-227 were essential for a functional CGRP-induced cAMP response. The effect of (H216A)CLR is due to a disruption to the cell surface transport or surface stability of the mutant receptor. In contrast, (K227A)CLR had wild-type expression and agonist affinity, suggesting a direct disruption to the downstream signal transduction mechanism of the CGRP receptor. Modeling suggests that the loop undergoes a significant shift in position during receptor activation, exposing a potential G-protein binding pocket. Lys-227 changes position to point into the pocket, potentially allowing it to interact with bound G-proteins. His-216 occupies a position similar to that of Tyr-136 in bovine rhodopsin, part of the DRY motif of the latter receptor. This is the first comprehensive analysis of an entire intracellular loop within the calcitonin family of G-protein-coupled receptor. These data help to define the structural and functional characteristics of the CGRP-receptor and of family B G-protein-coupled receptors in general. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

Analysis and optimisation of the performance of nonlinear optical communication systems

We investigate the feasibility of simultaneous suppressing of the amplification noise and nonlinearity, representing the most fundamental limiting factors in modern optical communication. To accomplish this task we developed a general design optimisation technique, based on concepts of noise and nonlinearity management. We demonstrate the immense efficiency of the novel approach by applying it to a design optimisation of transmission lines with periodic dispersion compensation using Raman and hybrid Raman-EDFA amplification. Moreover, we showed, using nonlinearity management considerations, that the optimal performance in high bit-rate dispersion managed fibre systems with hybrid amplification is achieved for a certain amplifier spacing – which is different from commonly known optimal noise performance corresponding to fully distributed amplification. Required for an accurate estimation of the bit error rate, the complete knowledge of signal statistics is crucial for modern transmission links with strong inherent nonlinearity. Therefore, we implemented the advanced multicanonical Monte Carlo (MMC) method, acknowledged for its efficiency in estimating distribution tails. We have accurately computed acknowledged for its efficiency in estimating distribution tails. We have accurately computed marginal probability density functions for soliton parameters, by numerical modelling of Fokker-Plank equation applying the MMC simulation technique. Moreover, applying a powerful MMC method we have studied the BER penalty caused by deviations from the optimal decision level in systems employing in-line 2R optical regeneration. We have demonstrated that in such systems the analytical linear approximation that makes a better fit in the central part of the regenerator nonlinear transfer function produces more accurate approximation of the BER and BER penalty. We present a statistical analysis of RZ-DPSK optical signal at direct detection receiver with Mach-Zehnder interferometer demodulation