Visualising Errors in Animal Pedigree Genotype Data

Genetic analysis of a breeding animal population involves determining the inheritance pattern of genotypes for multiple genetic markers across the individuals in the population pedigree structure. However, experimental pedigree genotype data invariably contains errors in both the pedigree structure and in the associated individual genotypes, introducing inconsistencies into the dataset, rendering them useless for further analysis. The resolution of these errors requires consideration of genotype inheritance patterns in the context of the pedigree structure. Existing pedigree visualisations are typically more suited to human pedigrees and are less suitable for large complex animal pedigrees which may exhibit cross generational inbreeding. Similarly, table‐based viewers of genotype marker data can highlight where errors become apparent but lack the functionality and interactive visual feedback to allow users to locate the origin of errors within the pedigree. In this paper, we detail a design study steered by biologists who work with pedigree data, and describe successive iterations through approaches and prototypes for viewing genotyping errors in the context of a displayed pedigree. We describe how each approach performs with real pedigree genotype data and why eventually we deemed them unsuitable. Finally, a novel prototype visualisation for pedigrees, which we term the ‘sandwich view’, is detailed and we demonstrate how the approach effectively communicates errors in the pedigree context, supporting the biologist in the error identification task.     

Similarity-based image organization and browsing using multi-resolution self-organizing map

An algorithm is presented in this paper to facilitate the exploration of large image collections based on visual similarities. Starting with an unordered and unannotated set of images, the algorithm first extracts the salient details into feature vectors using both color and gradient information. The feature vectors are then used to train a self-organizing map which maps high-dimensional feature vectors onto a 2D canvas so that images with similar feature vectors are grouped together. When users browse the image collection, an image collage is generated that selects and displays the most pertinent set of images based on which portion of the 2D canvas is currently in view. Flowing from an overview to details is a seamless operation controlled simply by pan and zoom, with representative images selected in a consistent and predictable way. To make organizing larger image collections practical in interactive time, the organization algorithm is designed to run in parallel on graphics processing units. Overall this paper presents an end-to-end solution that facilitates the surfing of image collections in a fresh way.     

Incremental Evolution in ANNs: Neural Nets which Grow

This paper explains the optimisation of neuralnetwork topology using Incremental Evolution;that is, by allowing the network to expand byadding to its structure. This method allows anetwork to grow from a simple to a complexstructure until it is capable of fulfilling itsintended function. The approach is somewhatanalogous to the growth of an embryo or theevolution of a fossil line through time, it istherefore sometimes referred to as anembryology or embryological algorithm. Thepaper begins with a general introduction,comparing this method to other competingtechniques such as The Genetic Algorithm, otherEvolutionary Algorithms and SimulatedAnnealing. A literature survey of previous workis included, followed by an extensive newframework for application of the technique.Finally, examples of applications and a generaldiscussion are presented.     

The experience of enchantment in human–computer interaction

Improving user experience is becoming something of a rallying call in human–computer interaction but experience is not a unitary thing. There are varieties of experiences, good and bad, and we need to characterise these varieties if we are to improve user experience. In this paper we argue that enchantment is a useful concept to facilitate closer relationships between people and technology. But enchantment is a complex concept in need of some clarification. So we explore how enchantment has been used in the discussions of technology and examine experiences of film and cell phones to see how enchantment with technology is possible. Based on these cases, we identify the sensibilities that help designers design for enchantment, including the specific sensuousness of a thing, senses of play, paradox and openness, and the potential for transformation. We use these to analyse digital jewellery in order to suggest how it can be made more enchanting. We conclude by relating enchantment to varieties of experience.An earlier version of this paper was presented at Chi’2004 Fringe.     

Automated computation and consistency checking of physical dimensions and units in scientific programs

Physical dimensions and units form an essential part of the specification of constants and variables occurring in scientific programs, yet no standard compilable programming language implements direct support for automated dimensional consistency checking and unit conversion. This paper describes a conceptual basis and prototype implementation for such support within the framework of the standard Fortran 90 language. This is accomplished via an external module supplying appropriate user data types and operator interfaces. Legacy Fortran 77 scientific software can be easily modified to compile and run as ‘dimension‐aware’ programs utilizing the proposed enhancements. Copyright © 2001 John Wiley & Sons, Ltd.     

Sodium metabisulfite and SO2 release: an under-recognized hazard among shrimp fishermen

Since the introduction of sodium metabisulfite as a food preservative, it has been associated with several idiosyncratic reactions (eg, bronchospasm, oculonasal symptoms, and urticaria/angioedema) in sulfite-sensitive individuals. The pathogenic mechanism of these reactions is not yet understood. We report the case of two crewmen on a shrimp trawler who were found dead in the ship's hold. Their deaths had occurred while they were applying dry sodium metabisulfite, referred to as "shrimp dip" in the shrimping industry. Postmortem examinations showed diffuse pulmonary edema consistent with death secondary to asphyxia. Associated findings were visceral congestion. Although it is possible to measure death from sodium metabisulfite with available records, its potential morbidity cannot be estimated. It is known that sodium metabisulfite can react with acids and water, releasing toxic sulfur dioxide (SO2) gas. In addition, SO2 gas reacts with respiratory tissue forming sulfureous acid, and inducing a pulmonary reaction causing hypoxemia. Furthermore, sodium metabisulfite, compared with sodium bisulfite, has a much greater propensity to release SO2 gas. We conclude that there is a need for improved education regarding the potential side effects of sodium metabisulfite, thus eliminating needless occupational morbidity and mortality.     

The role of inorganic polymer technology in the development of ‘green concrete’

The potential position of and drivers for inorganic polymers (“geopolymers”) as an element of the push for a sustainable concrete industry are discussed. These materials are alkali-activated aluminosilicates, with a much smaller CO₂ footprint than traditional Portland cements, and display very good strength and chemical resistance properties as well as a variety of other potentially valuable characteristics. It is widely known that the widespread uptake of geopolymer technology is hindered by a number of factors, in particular issues to do with a lack of long-term (20+ years) durability data in this relatively young research field. There are also difficulties in compliance with some regulatory standards in Europe and North America, specifically those defining minimum clinker content levels or chemical compositions in cements. Work on resolving these issues is ongoing, with accelerated durability testing showing highly promising results with regard to salt scaling and freeze–thaw cycling. Geopolymer concrete compliance with performance-based standards is comparable to that of most other high-strength concretes. Issues to do with the distinction between geopolymers synthesised for cement replacement applications and those tailored for niche ceramic applications are also discussed. Particular attention is paid to the role of free alkali and silicate in poorly-formulated systems and its deleterious effects on concrete performance, which necessitates a more complete understanding of the chemistry of geopolymerisation for the technology to be successfully applied. The relationship between CO₂ footprint and composition in comparison with Portland-based cements is quantified.     

Tracer studies on an aerated lagoon

The city of Palmerston North, New Zealand, has two aerated lagoons as its secondary treatment facility. Interest about treatment efficiency led to an investigation into the hydraulics in the second lagoon to determine if further optimisation was viable. A tracer study using rhodamine WT was undertaken to ascertain the stimulus response output. Samples were also taken at 24 points within the lagoon to determine the tracer concentration profile throughout the lagoon. The mean residence time was determined to be 39.9 h compared with a theoretical residence time of 55.4 h. Peak concentration of the tracer at the outlet occurred at 0.44 of the mean residence time. The results of the tracer study pointed to 28% of volume being dead space. A subsequent sludge survey indicated that 26% of the design volume of the lagoon was filled with sludge. While the curved geometry of the lagoon did not appear to impact the hydraulics the fact that the first aerator is confined in a relatively smaller area will have locally boosted the mixing energy input in this inlet zone. From interpretation of the tracer response and the tracer distribution profiles it appears that the aerators are mixing the influent into the bulk flow effectively in the front end of the lagoon and that there was no evidence of any substantive short-circuiting path of concentrated tracer around to the outlet. The tracer distribution profiles gave direct insight as to how the tracer was being transported within the pond and should be used more often when conducting tracer studies. Comparison with the literature indicated that the lagoon's hydraulic efficiency was on par with a baffled pond system and it would be expected that addition of several baffles to the lagoon would provide minimal further improvement.     

Clustering of high throughput gene expression data

High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis. However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data. It is also intended to introduce one of the main problems in bioinformatics – clustering gene expression data – to the operations research community.