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.     

Microgimbal torsion beam design using open, thin-walled crosssections

A thin-film micromolding process enabled the construction of microtorsional springs with unique cross-sectional designs by combining high-aspect-ratio beams with horizontal surface features. Cross sections such as T-bars, pi sections, and channels were utilized in creating torsional springs with low torsional stiffnesses and high in- and out-of-plane bending stiffnesses. Experimental modal analysis was used to determine torsional stiffnesses as low as 0.13 μN·m/deg with T-bar springs 45 μm tall, 50 μm wide, and 100 μm long. Springs of the same outer dimensions but with solid rectangular cross sections were calculated to have torsional stiffnesses of at least two orders of magnitude greater. Several microgimbals were constructed using the thin-film micromolding process with various torsional spring designs. Modal analysis was used to experimentally determine pitch and roll natural frequencies. Torsional stiffness models for open, thin-walled sections that included warping effects were developed and used to analytically predict the torsional natural frequencies of tested spring designs to within 20%     

Microstructure to substrate self-assembly using capillary forces

We have demonstrated the fluidic self-assembly of micromachined silicon parts onto silicon and quartz substrates in a preconfigured pattern with submicrometer positioning precision. Self-assembly is accomplished using photolithographically defined part and substrate binding sites that are complementary shapes of hydrophobic self-assembled monolayers. The patterned substrate is passed through a film of hydrophobic adhesive on water, causing the adhesive to selectively coat the binding sites. Next, the microscopic parts, fabricated from silicon-on-insulator wafers and ranging in size from 150×150×15 μm³ to 400×400×50 μm ³, are directed toward the substrate surface under water using a pipette. Once the hydrophobic pattern on a part comes into contact with an adhesive-coated substrate binding site, shape matching occurs spontaneously due to interfacial free energy minimization. In water, capillary forces of the adhesive hold the parts in place with an alignment precision of less than 0.2 μm. Permanent bonding of the parts onto quartz and silicon is accomplished by activating the adhesive with heat or ultraviolet light. The resulting rotational misalignment is within ~0.3°. Using square sites, 98-part arrays have been assembled in less than 1 min with 100% yield. The general microassembly approach described here may be applied to parts ranging in size from the nano- to milliscale, and part and substrate materials including semiconductors, glass, plastics, and metals     

High-aspect-ratio, molded microstructures with electrical isolation and embedded interconnects

 A thin film molding process was developed to enable the fabrication of monolithic micromechanical structures with built-in electrical isolation and embedded interconnects. High-aspect-ratio composite structures were created from undoped polysilicon, low stress nitride and doped polysilicon, in a dual micromolding process. These monolithic electro-mechanical microstructures are more resistant to thermal effects and misalignment errors compared to microsystems assembled from discrete elements. In addition, the microstructures are molded in a re-usable mold providing an economical advantage. A gimballed electrostatic microactuator was successfully fabricated using this process. Electrical isolation was achieved with a combination of low stress nitride and undoped polycrystalline silicon. Various isolation geometries were investigated. Current leakages of less than 1 nA at 30 V were measured for isolation structures 40 μm long and 80 μm tall. Received: 13 November 2000/Accepted: 16 November 2000     

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.     

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.     

Community intervention with the elderly: a social network approach

A technique is described for using the advantages of a social systems approach when working with elderly persons in psychiatric distress. The technique is based on the assumption that the solution to a variety of human predicaments lies within the collective instrumental and affective resources of the client's social network. The vehicle for accomplishing this objective is the "Network Session" during which a mental health professional meets with the elderly person and members of his/her social network to help resolve the difficulty. A case report demonstrating use of the technique is included.     

Evaluation of superposition technique for calculating cogging torque in permanent-magnet brushless machines

We evaluate the superposition method for calculating the cogging torque in permanent-magnet brushless machines, the resultant torque being synthesized from cogging torque components associated with a pair of magnets. Although finite-element analyses and measurements show that the resultant cogging torque cannot be synthesized directly from the torque components due to a single magnet, we use the concept of a fictitious single magnet to analytically establish the relationship between the cogging torque and key design parameters. The method is particularly useful in assessing the influence of the slot number and pole number combination.