Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Tourism as a contributor to development in Sri Lanka: An overview and a case study

General background is provided on the potential of tourism growth to contribute to economic development, paying particular attention to the experience of Sri Lanka. An overview of trends in inbound tourism to Sri Lanka is presented with particular consideration being given to its number of inbound tourist arrivals. Sri Lanka’s comparative position in international tourism markets, the composition of its tourist arrivals by area of origin, the extent of foreign earnings by the Sri Lankan tourism industry and variations in the amount of these earnings, and the extent of employment generation by this industry are examined. Regional aspects of the tourism industry in Sri Lanka are given special consideration, and this is followed by a report on the regional economic impact of tourism of Pinnawala Elephant Orphanage. This major tourist attraction near the edge of the Western Highlands of Sri Lanka is shown to make a significant contribution to economic decentralisation. A general discussion follows of tourism development in the Sri Lankan context. The main factors that have hindered tourism growth in Sri Lanka and its decentralisation are considered. Indications are that major impediment posed by civil disturbance and terrorism is at an end in Sri Lanka.

Polarization vision and its role in biological signaling

Visual pigments, the molecules in photoreceptors that initiate the process of vision, are inherently dichroic, differentially absorbing light according to its axis of polarization. Many animals have taken advantage of this property to build receptor systems capable of analyzing the polarization of incoming light, as polarized light is abundant in natural scenes (commonly being produced by scattering or reflection). Such polarization sensitivity has long been associated with behavioral tasks like orientation or navigation. However, only recently have we become aware that it can be incorporated into a high-level visual perception akin to color vision, permitting segmentation of a viewed scene into regions that differ in their polarization. By analogy to color vision, we call this capacity polarization vision. It is apparently used for tasks like those that color vision specializes in: contrast enhancement, camouflage breaking, object recognition, and signal detection and discrimination. While color is very useful in terrestrial or shallow-water environments, it is an unreliable cue deeper in water due to the spectral modification of light as it travels through water of various depths or of varying optical quality. Here, polarization vision has special utility and consequently has evolved in numerous marine species, as well as at least one terrestrial animal. In this review, we consider recent findings concerning polarization vision and its significance in biological signaling.

A family of perfect hashing methods

Minimal perfect hash functions are used for memory efficient storage and fast retrieval of items from static sets. We present an infinite family of efficient and practical algorithms for generating order preserving minimal perfect hash functions. We show that almost all members of the family construct space and time optimal order preserving minimal perfect hash functions, and we identify the one with minimum constants. Members of the family generate a hash function in two steps. First a special kind of function into an r-graph is computed probabilistically. Then this function is refined deterministically to a minimal perfect hash function. We give strong theoretical evidence that the first step uses linear random time. The second step runs in linear deterministic time. The family not only has theoretical importance, but also offers the fastest known method for generating perfect hash functions.

A comparison of the expressive communication skills of triplet, twin and singleton children

Few studies have focused on the language acquisition of higher multiple birth sets. In this study, the communication skills of 51 triplet children are described. The measures used were: mean length of utterance; type-token ratio; conversational nets; phoneme repertoire; and number of different types of phonological processes used. The data gained were used to compare the communication skills of triplets with those of twins, singletons and normative data available in the literature. Siblings within triplet sets were also compared using language samples obtained from adult-child interactions and when the three children were playing together. The results indicated that the triplets' early communication skills were different from those of both singletons and twins. The triplets' difficulties included delayed syntactic development, limited use of different language functions and delayed phonological development. In contrast, twins' communication profile is characterised by disordered phonological development.

Complete DNA sequence and gene organization of the mitochondrial genome of the liverfluke, Fasciola hepatica L. (Platyhelminthes; Trematoda)

The complete nucleotide sequence of the mitochondrial (mt) DNA molecule of the liverfluke, Fasciola hepatica (phylum Platyhelminthes, class Trematoda, family Fasciolidae), was determined, It comprises 14462 bp, contains 12 protein-encoding, 2 ribosomal and 22 transfer RNA genes, and is the second complete flatworm (and the first trematode) mitochondrial sequence to be described in detail. All of the genes are transcribed from the same strand. Of the genes typically found in mitochondrial genomes of eumetazoans, only atp8 is absent. The nad4L and nad4 genes overlap by 40 nt. Most intergenic sequences are very short. Two larger non-coding regions are present. The longer one (817 nt) is located between trnG and cox3 and consists of 8 identical tandem repeats of 85 nt, rich in G and C, followed by 1 imperfect repeat. The shorter non-coding region (187 nt) exhibits no special features and is separated from the longer region by trnG. The gene arrangement resembles that of some other trematodes including the eastern Asian Schistosoma species (and cyclophyllidean cestode species) but it is strikingly different from that of the African schistosomes, represented by Schistosoma mansoni. The genetic code is as inferred previously for flatworms. Transfer RNA genes range in length from 58 to 70 nt, their products producing characteristic 'clover leaf' structures, except for tRNA(S-VON) and tRNA(S-AGN) lacking the DHU arm.

Computational differentiation of N-terminal signal peptides and transmembrane helices

Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies. (C) 2003 Elsevier Inc. All rights reserved.

Is maximizing resilience compatible with established ecological goal functions?

Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] used a simple phytoplanktonzooplankton-nutrient model and a genetic algorithm to determine the parameter values that would maximize the value of certain goal functions. These goal functions were to maximize biomass, maximize flux, maximize flux to biomass ratio, and maximize resilience. It was found that maximizing goal functions maximized resilience. The objective of this study was to investigate whether the Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] result was indicative of a general ecosystem principle, or peculiar to the model and parameter ranges used. This study successfully replicated the Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] experiment for a number of different model types, however, a different interpretation of the results is made. A new metric, concordance, was devised to describe the agreement between goal functions. It was found that resilience has the highest concordance of all goal functions trialled. for most model types. This implies that resilience offers a compromise between the established ecological goal functions. The parameter value range used is found to affect the parameter versus goal function relationships. Local maxima and minima affected the relationship between parameters and goal functions, and between goal functions. (C) 2003 Elsevier B.V. All rights reserved.

Residential and lifestyle changes for adults with an intellectual disability in Queensland 1960-2001

As we celebrate 50 years of the Schonell Special Education Research Centre it is timely to consider changes that have occurred in the provision of residential services for people with an intellectual disability. Before the 1970s adults and children were cared for in large institutions using a medical model of care. In the mid-1970s a new developmental model based on education and training was implemented in response to the principle of normalisation and issues of social justice. The most dramatic changes have occurred in the last ten years with the decision to close large institutions and relocate residents into ordinary homes in the community. This paper describes changes in lifestyle for adults with an intellectual disability as a result of the move from institutional to community residential service provision. The Challinor Centre in Ipswich, Queensland, Australia provides examples of lifestyle changes that have occurred under different models of service provision during this time. Community living is described with research evidence validating the advantages of this type of service provision for residents with an intellectual disability. Outcomes have been documented through the use of group results and a case study of one individual following deinstitutionalisation describes the benefits of this new model of residential accommodation

Listening to the 'voices' of students with severe learning difficulties through a task-based approach to research and learning in physical education

In this article, Hayley Fitzgerald, Anne Jobling and David Kirk consider the physical education and sporting experiences of a group of students with severe learning difficulties. Their study is thought provoking, not only because of the important and somewhat neglected subject matter, but equally for the research approach adopted. The way in which the study engaged with the students and the insights gained from that engagement will be of particular interest to practitioner researchers.

Principals' and teachers' perceptions of learning disabilities: A study from Nara Prefecture, Japan

In this study, perceptions of learning disabilities were obtained from 128 principals and 123 teachers in the Nara Prefecture, Japan. A factor analysis indicated that five factors underlie perceptions of learning disabilities: changes in the family and social situation, insufficient knowledge of and support for learning disabilities, teachers' abilities and professional development, teachers' situation and governmental issues. Teachers' situation was perceived to be the main factor, whereas the least important factor was governmental issues. Teachers mainly indicated agreement on the factor of insufficient knowledge of and support for students with learning disabilities. Principals were more aware of governmental issues than teachers.

'I never imagined I'd have to teach these children': Providing authentic learning experiences for secondary pre-service teachers in teaching students with special needs

This article describes a collaborative and cross-curricula initiative undertaken in the School of Education at the University of Queensland, Brisbane, Australia. The project involved developing an integrated approach to providing professional year pre-service secondary teacher education students with experiences that would assist them to develop their knowledge and skills to teach students with special needs in their classrooms. These experiences were undertaken in the authentic teaching and learning context of a post-school literacy program for young adults with intellectual disabilities. In preliminary interviews pre-service teachers revealed that they lacked experience, knowledge and understanding related to teaching students with special needs, and felt that their teacher education program lacked focus in this field. This project was developed in response to these expressed needs. Through participating in the project, pre-service teachers' knowledge and understanding about working with students with diverse learning needs were developed as they undertook real and purposeful tasks in an authentic context.