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.

An approach to statistical lip modelling for speaker identification via chromatic feature extraction

This paper presents a novel technique for the tracking of moving lips for the purpose of speaker identification. In our system, a model of the lip contour is formed directly from chromatic information in the lip region. Iterative refinement of contour point estimates is not required. Colour features are extracted from the lips via concatenated profiles taken around the lip contour. Reduction of order in lip features is obtained via principal component analysis (PCA) followed by linear discriminant analysis (LDA). Statistical speaker models are built from the lip features based on the Gaussian mixture model (GMM). Identification experiments performed on the M2VTS¹ database, show encouraging results

The use of temporal speech and lip information for multi-modal speaker identification via multi-stream HMMs

Investigates the use of temporal lip information, in conjunction with speech information, for robust, text-dependent speaker identification. We propose that significant speaker-dependent information can be obtained from moving lips, enabling speaker recognition systems to be highly robust in the presence of noise. The fusion structure for the audio and visual information is based around the use of multi-stream hidden Markov models (MSHMM), with audio and visual features forming two independent data streams. Recent work with multi-modal MSHMMs has been performed successfully for the task of speech recognition. The use of temporal lip information for speaker identification has been performed previously (T.J. Wark et al., 1998), however this has been restricted to output fusion via single-stream HMMs. We present an extension to this previous work, and show that a MSHMM is a valid structure for multi-modal speaker identification

Identification of dispersion-dependent hexagonal cavity modes of an individual ZnO nanonail

The hexagonal resonator characteristics of an individual ZnO-nanonail’s head were investigated via spatially resolved cathodoluminescence (CL) at room temperature. The positions of most of distinct CL peaks in visible range were well matched to those of whispering gallery modes (WGMs) of a hexagonal dielectric cavity when we took birefringence and dispersion of refractive indices into account. The broad and weak peaks for TE polarization in long wavelength range were consistent with refractive-index values below the threshold for total internal inflection. CL peaks that were not matched to WGMs were identified as either triangular quasi-WGM or Fabry–Pérot resonance modes.

The emergent male shopper : an identification of male supermarket shopper types

Grocery shopping is a routine activity widely considered the responsibility of the female spouse, yet modern social and demographic shifts are causing men to engage in this task. This study develops a retail shopping typology of male grocery shoppers, employing a cluster analysis technique. Five distinct cohorts emerge from the data of eight constructs, measured by seventy one items. One new shopper type emerges from this research. This shopper presented as a younger man, at the commencement of their family lifecycle, attracted by a strong value offer, focusing on price and promotional discounts. Our research offers a contribution to the marketing, consumer behaviour and supermarket retailing disciplines in three ways. By examining and identifying male shopping behaviour in the context of grocery shopping, the development of a retail shopping typology of male grocery shoppers and the extension and employment of a cluster analysis in identifying distinct groups. This research has implications for gender, segmentation studies and consumer behaviour disciplines in regard to grocery shopping. The identification of specific groups of male grocery shoppers will enable grocery retailers to effectively implement important, targeted marketing strategies.

Responding to rapid change in higher education : enabling university departments responsible for work related programs through boundary spanning

Boundary spanning links organisations to one another in order to create mutually beneficial relationships; it is a concept developed and used in organisational theory but rarely used to understand organisational structures in higher education (Pruitt & Schwartz, 1999). Yet understanding boundary spanning activity has the capacity to help universities respond to demands for continuous quality improvement, and to increase capacity to react to environmental uncertainty. At a time of rapid change characterised by a fluctuating economic environment, globalisation, increased mobility, and ecological issues, boundary spanning could be viewed as a key element in assisting institutions in effectively understanding and responding to such change. The literature suggests that effective boundary spanning could help universities improve organisational performance, use of infrastructure and resources, intergroup relations, leadership styles, performance and levels of job satisfaction, technology transfer, knowledge creation, and feedback processes, amongst other things. Our research aims to put a face on boundary spanning (Miller, 2008) by contextualising it within organisational systems and structures in university departments responsible for work related programs i.e. Work Integrated Learning (WIL) and Co-operative Education (Co-op). In this paper these approaches are referred to collectively as work related programs. The authors formed a research team in Victoria, British Columbia in 2009 at a sponsored international research forum, Two Days in June. The purpose of the invitation-only forum was to investigate commonalities and differences across programs and to formulate an international research agenda for work related programs over the next five to ten years. Researchers from Queensland University of Technology, University of Cincinnati, Baden-Wuerttemberg Cooperative State University, University of Ottawa,and Dublin City University agreed that further research was needed into the impact stakeholders, organisational systems, structures, policies, and practices have on departments delivering work related programs. This paper illustrates how policy and practice across the five institutions can be better understood through the lens of boundary spanning. It is argued that boundary spanning is an area of theory and practice with great applicability to a better understanding of the activity of these departments. The paper concludes by proposing topics for future research to examine how boundary spanning can be used to better understand practice and change in work related programs.

Anchoring and exposing in the third place : regular identification at the boundaries of social realms

Harry’s is my favourite bar in my neighbourhood. It is a small wine bar, owned by three men in their late thirties and targeted at people like them; my gentrifying inner city neighbourhood’s 20 to 40 something urban middle class. Harry’s has seats along the bar, booths inside, and a courtyard out the back. The seating arrangements mean that larger groups tend to gather outside, groups of two to four spread around the location, and people by themselves, or in groups of two, tend to sit at the bar. I usually sit at the bar....

Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

Determinants of rapid weight gain during infancy: Baseline results from the NOURISH randomised controlled trial.

Background: Rapid weight gain in infancy is an important predictor of obesity in later childhood. Our aim was to determine which modifiable variables are associated with rapid weight gain in early life. Methods: Subjects were healthy infants enrolled in NOURISH, a randomised, controlled trial evaluating an intervention to promote positive early feeding practices. This analysis used the birth and baseline data for NOURISH. Birthweight was collected from hospital records and infants were also weighed at baseline assessment when they were aged 4-7 months and before randomisation. Infant feeding practices and demographic variables were collected from the mother using a self administered questionnaire. Rapid weight gain was defined as an increase in weight-for-age Z-score (using WHO standards) above 0.67 SD from birth to baseline assessment, which is interpreted clinically as crossing centile lines on a growth chart. Variables associated with rapid weight gain were evaluated using a multivariable logistic regression model. Results: Complete data were available for 612 infants (88% of the total sample recruited) with a mean (SD) age of 4.3 (1.0) months at baseline assessment. After adjusting for mother's age, smoking in pregnancy, BMI, and education and infant birthweight, age, gender and introduction of solid foods, the only two modifiable factors associated with rapid weight gain to attain statistical significance were formula feeding [OR=1.72 (95%CI 1.01-2.94), P= 0.047] and feeding on schedule [OR=2.29 (95%CI 1.14-4.61), P=0.020]. Male gender and lower birthweight were non-modifiable factors associated with rapid weight gain. Conclusions: This analysis supports the contention that there is an association between formula feeding, feeding to schedule and weight gain in the first months of life. Mechanisms may include the actual content of formula milk (e.g. higher protein intake) or differences in feeding styles, such as feeding to schedule, which increase the risk of overfeeding. Trial Registration: Australian Clinical Trials Registry ACTRN12608000056392

Mapping resilience : A framework for changing cities

Urban centres base their resilience on the ability to evolve and adapt as needed throughout their life. Although constantly developing, changing and subsuming nature for its needs, the current age of environmental awareness requires that cities progress in a more conscious and considered way. While they have become the dominant form of human habitation, there now exists a need to integrate 'green' solutions into urban centres to address social, physical and environmental wellbeing. The means of implementing the vast array of possible solutions without negative impacts is not clear; cities are complex systems, layering meaning, history and cultural memory ‐ they are a manifestation of shared cultural values, and as such, they do not allow a tabula rasa approach of 'blanket' solutions. All around us, cities are continuing to develop and change, and although their form is varied ‐ sprawling cities with density and sustainability problems; or collapsing cities with 'dead' centres and dilapidated districts – a common issue is the resilience of the local identity. The strength or resilience of cities lies in the elements which have become fixed points in the urban structure, giving character and identity to a shared urban experience. These elements need to be identified and either maintained or revitalised. Similarly, the identification of urban elements which can most viably be modified without compromising character and identity of place, will assist in making concrete contributions to increasing both the sustainability and experience of cities, making them more resilient. Through an examination of case studies, this paper suggests a framework to inform urban renewal assessing the widespread elements which generate an urban identity, beyond the traditional approach of heritage conservation for cultural or tourist purposes. The rapid contemporary alteration of urban structures requires an innovative methodology which satisfies on one side the need of new sustainable performances and, on the other, the resilience of the local character.