SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Pattern recognition using invariants defined from higher order spectra : 2-D image inputs

A new algorithm for extracting features from images for object recognition is described. The algorithm uses higher order spectra to provide desirable invariance properties, to provide noise immunity, and to incorporate nonlinearity into the feature extraction procedure thereby allowing the use of simple classifiers. An image can be reduced to a set of 1D functions via the Radon transform, or alternatively, the Fourier transform of each 1D projection can be obtained from a radial slice of the 2D Fourier transform of the image according to the Fourier slice theorem. A triple product of Fourier coefficients, referred to as the deterministic bispectrum, is computed for each 1D function and is integrated along radial lines in bifrequency space. Phases of the integrated bispectra are shown to be translation- and scale-invariant. Rotation invariance is achieved by a regrouping of these invariants at a constant radius followed by a second stage of invariant extraction. Rotation invariance is thus converted to translation invariance in the second step. Results using synthetic and actual images show that isolated, compact clusters are formed in feature space. These clusters are linearly separable, indicating that the nonlinearity required in the mapping from the input space to the classification space is incorporated well into the feature extraction stage. The use of higher order spectra results in good noise immunity, as verified with synthetic and real images. Classification of images using the higher order spectra-based algorithm compares favorably to classification using the method of moment invariants

Evidence for u.v. induction of CDKN2 mutations in melanoma cell lines

The CDKN2 gene, encoding the cyclin dependent kinase inhibitor p16, is a tumour suppressor gene involved in melanoma and maps to chromosome band 9p22. Mutations or interstitial deletions of this gene have been found both in the germline of familial melanoma cases and somatically in melanoma cell lines. Previous mutation analyses of melanoma cell lines have indicated a high frequency of C:G to T:A transitions, with all of these mutations occurring at dipyrimidine sites. Including three melanoma cell lines carrying tandem CC to TT mutations, the spectrum of mutations so far reported indicates a possible role for u.v. radiation in the mutagenesis of this gene in some tumours. To further examine this hypothesis we have characterised mutations of the CDKN2 gene in 30 melanoma cell lines. Nineteen lines carried complete or partial homozygous deletions of the gene. Of the remaining cell lines, eight were shown by direct sequencing of PCR products from exon 1 and exon 2 to carry a total of nine different mutations of CDKN2. Two cell lines carried tandem CC to TT mutations and a high rate of C:G to T:A transitions was observed. This study provides further evidence for the role of u.v. light in the genesis of melanoma, with one target being the CDKN2 tumour suppressor gene.

Mutations in exon 3 of the beta-catenin gene are rare in melanoma cell lines

Mutations in exon 3 of the CTNNB1 gene encoding beta-catenin have been reported in colorectal cancer cell lines and tumours. Although one study reported mutations or deletions affecting beta-catenin in 20% of melanoma cell lines, subsequent reports detected a much lower frequency of aberrations in uncultured melanomas. To determine whether this difference in mutation frequency reflected an in vitro culturing artefact, exon 3 of CTNNB1 was screened in a panel of 62 melanoma cell lines. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was performed to detect intragenic deletions affecting exon 3. One out of 62 (1.6%) cell lines was found to carry a mutation, indicating that aberration of the Wnt-1/wingless pathway through activation of beta-catenin is a rare event, even in melanoma cell lines.

PTEN inactivation is rare in melanoma tumours but occurs frequently in melanoma cell lines

Deletions detected in cytogenetic and loss of heterozygosity (LOH) studies indicate that at least one tumour suppressor gene maps to the long arm of chromosome 10. Previous deletion mapping studies have observed LOH on 10q in about 30% of melanomas analysed. The PTEN gene, mapping to chromosome band 10q23.3, encodes a protein with both lipid and protein phosphatase activity. Somatic mutations and deletions in have been detected in a variety of cell lines and tumours, including melanoma samples. We performed mutation analyses and extensive allelic loss studies to investigate the role this gene plays in melanoma pathogenesis. We found that a total of 34 out of 57 (60%) melanoma cell lines carried hemizygous deletions of chromosome 10q encompassing the PTEN locus. A further three cell lines carried smaller deletions excluding PTEN. Inactivation of both PTEN alleles by exon-specific homozygous deletion or mutation was observed in 13 out of 57 (23%) melanoma cell lines. The mutation spectrum observed does not indicate an important role for ultraviolet radiation in the genesis of these mutations, and evidence from three cell lines supports the acquisition of PTEN aberrations in culture. Ten out of 49 (20%) matched melanoma tumour/normal samples harboured hemizygous deletions of either the whole chromosome or most of the long arm. Mutations within were detected in only one of the 10 tumours demonstrating LOH at 10q23 that were analysed. These results suggest that PTEN inactivation may be important for the propagation of melanoma cells in culture, and that another chromosome 10 tumour suppressor gene may be important for melanoma pathogenesis.

Diversity in product familiarity across younger and older adults

This paper reports on the findings of a completed experiment examining levels of familiarity in younger and older adults. Research has shown that older adults use products less intuitively than younger adults, and that familiarity is an essential element of intuitive interaction. This finding influenced the decision to focus on familiarity and to investigate why older adults use products less intuitively than younger adults. By identifying and understanding the differences in familiarity, it is hypothesised that designers will be able to design more usable products for older adults. An empirical study was conducted, investigating the differences in familiarity between younger and older adults with contemporary products. Younger adults demonstrate significantly higher levels of familiarity compared to older adults, and the three groups of older adults demonstrated no significant differences between them. The implications of this finding is discussed.

A software tool for simulating spatial separation and kinetics in biological membranes

Self-segregation and compartimentalisation are observed experimentally to occur spontaneously on live membranes as well as reconstructed model membranes. It is believed that many of these processes are caused or supported by anomalous diffusive behaviours of biomolecules on membranes due to the complex and heterogeneous nature of these environments. These phenomena are on the one hand of great interest in biology, since they may be an important way for biological systems to selectively localize receptors, regulate signaling or modulate kinetics; and on the other, they provide an inspiration for engineering designs that mimick natural systems. We present an interactive software package we are developing for the purpose of simulating such processes numerically using a fundamental Monte Carlo approach. This program includes the ability to simulate kinetics and mass transport in the presence of either mobile or immobile obstacles and other relevant structures such as liquid-ordered lipid microdomains. We also present preliminary simulation results regarding the selective spatial localization and chemical kinetics modulating power of immobile obstacles on the membrane, obtained using the program.

Grocery product pricing and Australian supermarket consumers : gender differences in perceived importance levels

Grocery shopping is an essential and routine activity. Although long regarded the responsibility of the female spouse, modern social and demographic shifts are causing men to become more engaged in this task. This is the first study to analyse gender differences with respect to the criterion of grocery product price within an Australian supermarket retail environment. A stratified sample of 140 male and 140 female grocery shoppers was surveyed. Results showed that men considered price attributes of products as being significantly lower in importance than did women. Additionally, men displayed lower levels of price nvolvement, reported referencing shelf price to a lesser extent, and gave lesser consideration to promotional tactics focusing on low price. Although men on average buy fewer items than do women, they spend more money for each item they purchase. This higher expenditure per item appears to be driven, at least in part, by a lack of price referencing. This research has implications for gender studies and consumer behaviour disciplines in relation to grocery shopping.

Feasibility of using health data sources to inform product safety surveillance in Queensland : a report for the Queensland Injury Prevention Council

This report provides an evaluation of the current available evidence-base for identification and surveillance of product-related injuries in children in Queensland. While the focal population was children in Queensland, the identification of information needs and data sources for product safety surveillance has applicability nationally for all age groups. The report firstly summarises the data needs of product safety regulators regarding product-related injury in children, describing the current sources of information informing product safety policy and practice, and documenting the priority product surveillance areas affecting children which have been a focus over recent years in Queensland. Health data sources in Queensland which have the potential to inform product safety surveillance initiatives were evaluated in terms of their ability to address the information needs of product safety regulators. Patterns in product-related injuries in children were analysed using routinely available health data to identify areas for future intervention, and the patterns in product-related injuries in children identified in health data were compared to those identified by product safety regulators. Recommendations were made for information system improvements and improved access to and utilisation of health data for more proactive approaches to product safety surveillance in the future.

Product labelling can confer sustained increases in expected and actual satiety

Expected satiety has been shown to play a key role in decisions around meal size. Recently it has become clear that these expectations can also influence the satiety that is experienced after a food has been consumed. As such, increasing the expected and actual satiety a food product confers without increasing its caloric content is of importance. In this study we sought to determine whether this could be achieved via product labelling. Female participants (N=75) were given a 223-kcal yoghurt smoothie for lunch. In separate conditions the smoothie was labelled as a diet brand, a highly-satiating brand, or an ‘own brand’ control. Expected satiety was assessed using rating scales and a computer-based ‘method of adjustment’, both prior to consuming the smoothie and 24 hours later. Hunger and fullness were assessed at baseline, immediately after consuming the smoothie, and for a further three hours. Despite the fact that all participants consumed the same food, the smoothie branded as highly-satiating was consistently expected to deliver more satiety than the other ‘brands’; this difference was sustained 24 hours after consumption. Furthermore, post-consumption and over three hours, participants consuming this smoothie reported significantly less hunger and significantly greater fullness. These findings demonstrate that the satiety that a product confers depends in part on information that is present around the time of consumption. We suspect that this process is mediated by changes to expected satiety. These effects may potentially be utilised in the development of successful weight-management products.

Ageing and use of complex product interfaces

This paper presents an experiment designed to investigate if redundancy in an interface has any impact on the use of complex interfaces by older people and people with low prior-experience with technology. The important findings of this study were that older people (65+ years) completed the tasks on the Words only based interface faster than on Redundant (text and symbols) interface. The rest of the participants completed tasks significantly faster on the Redundant interface. From a cognitive processing perspective, sustained attention (one of the functions of Central Executive) has emerged as one of the important factors in completing tasks on complex interfaces faster and with fewer of errors.

Using visuals to explore the contextual aspects of user-product interactions

Experience underlies all kinds of human knowledge and it is dependent on context. People’s experience within a particular context-of-use determines how they interact with products. Methods employed in this research to elicit human experience have included the use of visuals. This paper describes two empirical studies that employed visual representation of concepts as a means to explore the experiential and contextual component of user- product interactions. One study employed visuals that the participants produced during the study. The other employed visuals that the researcher used as prompts during a focus group session. This paper demonstrates that using visuals in design research is valuable for exploring and understanding the contextual aspects of human experience and its influence on people’s concepts of product use.