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.

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 impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.

Harm minimization in a prohibition context - Australia

Australia ranks high internationally in the prevalence of cannabis and other illicit drug use, with the prevalence of all illicit drug use increasing since the 1970s. There are two distinctive features associated with harms from injecting drug use-high rates of death from heroin overdose and low rates of HIV infection. Australia has largely avoided a punitive and moralistic drug policy, developing instead harm minimization strategies and a robust treatment framework embedded in a strong law enforcement regime. Two illustrations of Australian drug policy are presented: legislation that provides for the expiation of simple cannabis offences by payment of a fine and the widespread implementation of agonist maintenance treatment for heroin dependence.

On learning context-free and context-sensitive languages

The long short-term memory (LSTM) is not the only neural network which learns a context sensitive language. Second-order sequential cascaded networks (SCNs) are able to induce means from a finite fragment of a context-sensitive language for processing strings outside the training set. The dynamical behavior of the SCN is qualitatively distinct from that observed in LSTM networks. Differences in performance and dynamics are discussed.

Telemedicine for new neurological outpatients: putting a randomized controlled trial in the context of everyday practice

In a retrospective review, the telemedical management of 65 outpatients from a randomized controlled trial (RCT) of telemedicine for non-urgent referrals to a consultant neurologist was compared with the management of 76 patients seen face to face in the same trial, with that of 150 outpatients seen in the neurology clinics of district general hospitals and with that of 102 neurological outpatients seen by general physicians. Outcome measures were the numbers of investigations and of patient reviews. The telemedicine group did not differ significantly from the 150 patients seen face to face by neurologists in hospital clinics in terms of either the number of investigations or the number of reviews they received. Patients from the RCT seen face to face had significantly fewer investigations but a similar number of reviews to the other 150 patients seen face to face by neurologists (the disparity in the number of investigations may explain the negative result for telemedicine in that RCT). Patients with neurological symptoms assessed by general physicians had significantly more investigations and were reviewed significantly more often than all the other groups. Patients from the RCT seen by telemedicine were not managed significantly differently from those seen face to face by neurologists in hospital clinics but had significantly fewer investigations and follow-ups than those patients managed by general physicians. The results suggest that management of new neurological outpatients by neurologists using telemedicine is similar to that by neurologists using a face-to-face consultation, and is more efficient than management by general physicians.

Communism and Carnival: Ralph de Boissieres Crown Jewel and its Australian Context

The Australasian Book Society (ABS) was established in Melbourne in 1952 by a small group ofleft-leaning writers, unionists and literary supporters. It was inspired in part by the success of Frank Hardy's scandalous novel of Labar betrayal, Power Without Glory, which in 1950 had been published independently - and printed secretly - outside the commercial publishing networks. Many of those involved were communists but although the ABS came to operate in accord ,..rith Communist Party cultural politics it was never Simply a Party front nor did it publish only communist writers or communist texts. For the most part it operated under a broader notion of 'progressive' , nationalist or democratic literature.

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.