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.

Cooperative fishing interactions between Aboriginal Australians and dolphins in eastern Australia

Published eyewitness accounts and stories form Aboriginal Australians are used to provide an overview of the geographical extent and characteristics of cooperative fishing between Aboriginal Australians and dolphins in eastern Australia. These sources indicate that cooperative fishing was geographically widespread in eastern Australia, involved both bottlenose dolphins and orcas, and had a significance (emotional and Spiritual) to Aboriginal people beyond the acquisition of food. These fishing interactions represent both context and precedent for the economic and emotional-objectives of contemporary human-dolphin interactions such as dolphin provisioning. (C) 2002 International Society for Anthrozoology.

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.

The long-term effects of cooperative learning on children's behaviour and interactions

This study investigates the long-term effects of training in small-group and interpersonal behaviours on children's behaviours and interactions as they worked in small groups two years after they were initially trained. Forty-eight third grade children, who had been trained two years previously in cooperative group behaviours, were assigned to the Trained condition and 44 third grade children who had not previously been trained were assigned to the Untrained condition. The children in the trained and untrained groups were reconstituted from the pool of students who had participated previously in either trained or untrained group activities. The results showed that there was a long-term training effect with the children in the Trained groups demonstrating more cooperative behaviour and providing more explanations in response to requests for help than their untrained peers.

The residual effects of cooperative-learning experiences: A two-year follow-up

The author investigated how training in small-group and interpersonal behaviors affected children's behavior and interactions as they worked in small groups 2 years later. The authors assigned 52 fifth graders, who had been trained 2 years previously in cooperative group behaviors, to the trained condition and 36 fifth graders, who had not previously been trained, to the untrained condition. Both were reconstituted from the pool of students who had participated previously in group activities. The results showed a residual training effect, with the children in the trained groups being more cooperative and helpful than their untrained peers.

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.

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.

The tree cut and merge algorithm for estimation of network reliability

This article presents Monte Carlo techniques for estimating network reliability. For highly reliable networks, techniques based on graph evolution models provide very good performance. However, they are known to have significant simulation cost. An existing hybrid scheme (based on partitioning the time space) is available to speed up the simulations; however, there are difficulties with optimizing the important parameter associated with this scheme. To overcome these difficulties, a new hybrid scheme (based on partitioning the edge set) is proposed in this article. The proposed scheme shows orders of magnitude improvement of performance over the existing techniques in certain classes of network. It also provides reliability bounds with little overhead.

A genetic algorithm/method of moments approach to the optimization of an RF coil for MRI applications - Theoretical considerations - Abstract

A Combined Genetic Algorithm and Method of Moments design methods is presented for the design of unusual near-field antennas for use in Magnetic Resonance Imaging systems. The method is successfully applied to the design of an asymmetric coil structure for use at 190MHz and demonstrates excellent radiofrequency field homogeneity.

Brazil and the institutionalization of South America: from hemispheric estrangement to cooperative hegemony

This article argues that Brazil went from a posture of estrangement in relation to the hemispheric project represented by the Free Trade Area of the Americas (FTAA) to a strategy of cooperative hegemony aimed at institutionalizing the South American space and increasing the costs of the FTAA for the United States. Although Brazil was initially isolated, US lack of leadership combined with events at the subregional level ended up turning the tide in the direction of Brazilian interests. These factors help to understand the current institutional configuration of South America.

Automated traffic route identification through the shared nearest neighbour algorithm

Many organisations need to extract useful information from huge amounts of movement data. One example is found in maritime transportation, where the automated identification of a diverse range of traffic routes is a key management issue for improving the maintenance of ports and ocean routes, and accelerating ship traffic. This paper addresses, in a first stage, the research challenge of developing an approach for the automated identification of traffic routes based on clustering motion vectors rather than reconstructed trajectories. The immediate benefit of the proposed approach is to avoid the reconstruction of trajectories in terms of their geometric shape of the path, their position in space, their life span, and changes of speed, direction and other attributes over time. For clustering the moving objects, an adapted version of the Shared Nearest Neighbour algorithm is used. The motion vectors, with a position and a direction, are analysed in order to identify clusters of vectors that are moving towards the same direction. These clusters represent traffic routes and the preliminary results have shown to be promising for the automated identification of traffic routes with different shapes and densities, as well as for handling noise data.

Automation & control remote laboratory: evaluating a cooperative methodology

This paper presents a study carried out in order to evaluate the students' perception in the development and use of remote Control and Automation education kits developed by two Universities. Three projects, based on real world environments, were implemented, being local and remotely operated. Students implemented the kits using the theoretical and practical knowledge, being the teachers a catalyst in the learning process. When kits were operational, end-user students got acquainted to the kits in the course curricula units. It is the author's believe that successful results were achieved not only in the learning progress on the Automation and Control fields (hard skills) but also on the development of the students soft skills, leading to encouraging and rewarding goals, motivating their future decisions and promoting synergies in their work. The design of learning experimental kits by students, under teacher supervision, for future use in course curricula by enduser students is an advantageous and rewarding experience.