An algorithm to predict 3 ' intron splice sites in Plasmodium falciparum genomic sequences

A new algorithm, PfAGSS, for predicting 3' splice sites in Plasmodium falciparum genomic sequences is described. Application of this program to the published P. falciparum chromosome 2 and 3 data suggests that existing programs result in a high error rate in assigning 3' intron boundaries. (C) 2001 Elsevier Science B.V. All rights reserved.

A simulated annealing algorithm for finding consensus sequences

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new algorithm. For comparison, we also present similar results obtained using ClustalW. The new algorithm outperforms ClustalW in many cases.

Genetic sources of covariation among P3(00) and online performance variables in a delayed-response working memory task

Genetic and environmental sources of covariation among the P3(00) and online performance elicited in a delayed-response working memory task, and psychometric IQ assessed by the multidimensional aptitude battery, were examined in an adolescent twin sample. An association between frontal P3 latency and task performance (phenotypic r = -0.33; genotypic r = -0.49) was indicated, with genes (i.e. twin status) accounting for a large part of the covariation ( > 70%). In contrast, genes influencing P3 amplitude mediated only a small part (2%) of the total genetic variation in task performance. While task performance mediated 15% of the total genetic variation in IQ (phenotypic r = 0.22; genotypic r = 0.39) there was no association between P3 latency and IQ or P3 amplitude with IQ. The findings provide some insight into the inter-relationships among psychophysiological, performance and psychometric measures of cognitive ability, and provide support for a levels-of-processing genetic model of cognition where genes act on specific sub-components of cognitive processes.

A monolithic smoothing-gap algorithm for contact-impact based on the signed distance function

A new algorithm has been developed for smoothing the surfaces in finite element formulations of contact-impact. A key feature of this method is that the smoothing is done implicitly by constructing smooth signed distance functions for the bodies. These functions are then employed for the computation of the gap and other variables needed for implementation of contact-impact. The smoothed signed distance functions are constructed by a moving least-squares approximation with a polynomial basis. Results show that when nodes are placed on a surface, the surface can be reproduced with an error of about one per cent or less with either a quadratic or a linear basis. With a quadratic basis, the method exactly reproduces a circle or a sphere even for coarse meshes. Results are presented for contact problems involving the contact of circular bodies. Copyright (C) 2002 John Wiley Sons, Ltd.

Well-formedness judgment: A comparison of offline and online performance in Broca's aphasics

0na eg rcarmitimcaal tfieca tcuorem opfr ethhee nospieornat iodneafli cdietf i(nAitiCoDn )o ft hthaet frequently co-occurs with Broca’s aphasia is above-chance performance on well-formedness judgment tasks for many syntactic constructions, but impaired performance where syntactic binding of traces to their antecedents occurs. However, the methodologies used to establish this aspect of the performance profile of the ACD have been predominantly offline. Offline well-formedness tasks entail extralinguistic processing (e.g. perception, attention, short-term memory, conscious reflection) in varying amounts and the influence of such processes on parsing mechanisms is yet to be fully established. In order to (a) further understand the role of extra-linguistic processing on parsing, and (b) gain a more direct insight into the online nature of parsing in Broca’s aphasia, 8 subjects underwent a series of wellformedness judgment investigations using both offline and online test batteries. The sentence types and error types used were motivated by three current theories about the nature of the ACD, namely, the Trace-Based Account (Grodzinsky, 2000), the Mapping Hypothesis (Linebarger et al., 1983) and Capacity proposals (e.g. Frazier & Friederici, 1991). The results from the present investigation speak directly to the three aforementioned theories and also demonstrate the important role that extralinguistic processing plays during offline assessment. The clinical implications of the different outcomes from the offline vs. online tasks are also discussed.

A subset-oriented algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search. (C) 2002 Elsevier Science Ltd. All rights reserved.

'Vigilant Hospitality': The Online Imperative and Teaching Cultural Studies

Information technology (IT) sees information as a fluid, to be stored, regulated and exchanged. This is a profoundly economic model, whose dreams are those of the marketplace – and now, university managers. But no teacher, of course, holds that teaching can be reduced to the movement of information from one point to another. Teaching is never quite absorbed into the models of IT. Where they meet, we do not have the utopia of the virtual classroom, at last freed from the strictures of timetables and the face-to-face; we have, rather, the grinding of two radically irreducible models. This has nothing to do with Luddism; on the contrary, it is the value and necessity of IT for us at present, as teachers. At a time when the tertiary sector’s massive investment in IT is motivated in part by its own dream of the teacherless classroom, one of the pressing tasks for us may be simply to argue as rigorously as we can the structural necessity of our own position as teachers, without nostalgia or humanist sentimentality.

An augmented Lanczos algorithm for the efficient computation of a dot-product of a function of a large sparse symmetric matrix

The Lanczos algorithm is appreciated in many situations due to its speed. and economy of storage. However, the advantage that the Lanczos basis vectors need not be kept is lost when the algorithm is used to compute the action of a matrix function on a vector. Either the basis vectors need to be kept, or the Lanczos process needs to be applied twice. In this study we describe an augmented Lanczos algorithm to compute a dot product relative to a function of a large sparse symmetric matrix, without keeping the basis vectors.