Sensitivity of edge detection methods for quantifying cell migration assays

Quantitative imaging methods to analyze cell migration assays are not standardized. Here we present a suite of two–dimensional barrier assays describing the collective spreading of an initially–confined population of 3T3 fibroblast cells. To quantify the motility rate we apply two different automatic image detection methods to locate the position of the leading edge of the spreading population after 24, 48 and 72 hours. These results are compared with a manual edge detection method where we systematically vary the detection threshold. Our results indicate that the observed spreading rates are very sensitive to the choice of image analysis tools and we show that a standard measure of cell migration can vary by as much as 25% for the same experimental images depending on the details of the image analysis tools. Our results imply that it is very difficult, if not impossible, to meaningfully compare previously published measures of cell migration since previous results have been obtained using different image analysis techniques and the details of these techniques are not always reported. Using a mathematical model, we provide a physical interpretation of our edge detection results. The physical interpretation is important since edge detection algorithms alone do not specify any physical measure, or physical definition, of the leading edge of the spreading population. Our modeling indicates that variations in the image threshold parameter correspond to a consistent variation in the local cell density. This means that varying the threshold parameter is equivalent to varying the location of the leading edge in the range of approximately 1–5% of the maximum cell density.

Parametric and generative methods with building information modelling : connecting BIM with explorative design modelling

Parametric and generative modelling methods are ways in which computer models are made more flexible, and of formalising domain-specific knowledge. At present, no open standard exists for the interchange of parametric and generative information. The Industry Foundation Classes (IFC) which are an open standard for interoperability in building information models is presented as the base for an open standard in parametric modelling. The advantage of allowing parametric and generative representations are that the early design process can allow for more iteration and changes can be implemented quicker than with traditional models. This paper begins with a formal definition of what constitutes to be parametric and generative modelling methods and then proceeds to describe an open standard in which the interchange of components could be implemented. As an illustrative example of generative design, Frazer’s ‘Reptiles’ project from 1968 is reinterpreted.

Book review: "Qualitative Health Psychology. Theories and Methods" Michael Murray and Kerry Chamberlain (Eds.)

Qualitative Health Psychology aims to contribute to the debate about the nature of psychology and of science through ‘an examination of the role of qualitative research within health psychology’ (p. 3). The editors, in bringing together contributors from the UK, Ireland, Canada, Brazil, New Zealand and Australia, have compiled a text that reflects different uses of qualitative health research in diverse social and cultural contexts. Structured into three parts, the book encompasses key theoretical and methodological issues in qualitative research in its attempt to encourage broad epistemological debate within health psychology.

Poststructuralism, qualitative methodology, and public health : research methods as a legitimization strategy for knowledge

The appearance of poststructuralism as a research methodology in public health literature raises questions about the history and purpose of this research. We examine (a) some aspects of the history of qualitative methods and their place within larger social and research domains, and (b) the purposes of a public health research that employs poststructuralist philosophy delineating the methodological issues that require consideration in positing a poststructural analysis. We argue against poststructuralism becoming a research methodology deployed to seize the pubic health debate, rather than being employed for its own particular critical strengths.

The naturally imperfect form : investigations of the application of digital sculpting methods - extracted art : incorporating and translating ‘found art’ into the medium of digital sculpture

This dissertation analyses how physical objects are translated into digital artworks using techniques which can lead to ‘imperfections’ in the resulting digital artwork that are typically removed to arrive at a ‘perfect’ final representation. The dissertation discusses the adaptation of existing techniques into an artistic workflow that acknowledges and incorporates the imperfections of translation into the final pieces. It presents an exploration of the relationship between physical and digital artefacts and the processes used to move between the two. The work explores the 'craft' of digital sculpting and the technology used in producing what the artist terms ‘a naturally imperfect form’, incorporating knowledge of traditional sculpture, an understanding of anatomy and an interest in the study of bones (Osteology). The outcomes of the research are presented as a series of digital sculptural works, exhibited as a collection of curiosities in multiple mediums, including interactive game spaces, augmented reality (AR), rapid prototype prints (RP) and video displays.

Developing national level informatics competencies for undergraduate nurses : methodological approaches from Australia and Canada

Health information systems are being implemented in countries by governments and regional health authorities in an effort to modernize healthcare. With these changes, there has emerged a demand by healthcare organizations for nurses graduating from college and university programs to have acquired nursing informatics competencies that would allow them to work in clinical practice settings (e.g. hospitals, clinics, home care etc). In this paper we examine the methods employed by two different countries in developing national level nursing informatics competencies expected of undergraduate nurses prior to graduation (i.e. Australia, Canada). This work contributes to the literature by describing the science and methods of nursing informatics competency development at a national level.

Sample size considerations and augmentation of computer experiments

Computer Experiments, consisting of a number of runs of a computer model with different inputs, are now common-place in scientific research. Using a simple fire model for illustration some guidelines are given for the size of a computer experiment. A graph is provided relating the error of prediction to the sample size which should be of use when designing computer experiments. Methods for augmenting computer experiments with extra runs are also described and illustrated. The simplest method involves adding one point at a time choosing that point with the maximum prediction variance. Another method that appears to work well is to choose points from a candidate set with maximum determinant of the variance covariance matrix of predictions.

Fixed failure rate ambiguity validation methods for GPS and compass

Ambiguity resolution plays a crucial role in real time kinematic GNSS positioning which gives centimetre precision positioning results if all the ambiguities in each epoch are correctly fixed to integers. However, the incorrectly fixed ambiguities can result in large positioning offset up to several meters without notice. Hence, ambiguity validation is essential to control the ambiguity resolution quality. Currently, the most popular ambiguity validation is ratio test. The criterion of ratio test is often empirically determined. Empirically determined criterion can be dangerous, because a fixed criterion cannot fit all scenarios and does not directly control the ambiguity resolution risk. In practice, depending on the underlying model strength, the ratio test criterion can be too conservative for some model and becomes too risky for others. A more rational test method is to determine the criterion according to the underlying model and user requirement. Miss-detected incorrect integers will lead to a hazardous result, which should be strictly controlled. In ambiguity resolution miss-detected rate is often known as failure rate. In this paper, a fixed failure rate ratio test method is presented and applied in analysis of GPS and Compass positioning scenarios. A fixed failure rate approach is derived from the integer aperture estimation theory, which is theoretically rigorous. The criteria table for ratio test is computed based on extensive data simulations in the approach. The real-time users can determine the ratio test criterion by looking up the criteria table. This method has been applied in medium distance GPS ambiguity resolution but multi-constellation and high dimensional scenarios haven't been discussed so far. In this paper, a general ambiguity validation model is derived based on hypothesis test theory, and fixed failure rate approach is introduced, especially the relationship between ratio test threshold and failure rate is examined. In the last, Factors that influence fixed failure rate approach ratio test threshold is discussed according to extensive data simulation. The result shows that fixed failure rate approach is a more reasonable ambiguity validation method with proper stochastic model.

Point of no return : exploring katabatic narrative and deterritorialisation in the Australian outback novel

This thesis consists of the novel Brolga and an exegesis examining in what ways the ideas of katabasis and deterritorialisation inform an understanding of descent narratives in contemporary Australian outback fiction. When writing the creative piece, it was observed that Joseph Campbell’s Hero’s Journey was an imprecise model for my manuscript and indeed for many of the contemporary novels I had read written in similar outback settings. On analysis a better fit lies in the idea of a heroic journey from which there is no clear return from the underworld. This narrative form is defined in this thesis as a katabatic narrative. To unpack this narrative trope, the inverse of territoriality, deterritorialisation, is used as a lens to examine the complex thematic and symbolic resonances of the outback in both Brolga and analogous works of contemporary outback fiction.

Capitalising on mixed methods research : design, examples, and practice

Overview: - Development of mixed methods research - Benefits and challenges of “mixing” - Different models - Good design - Two examples - How to report? - Have a go!

A Bayesian approach to the determination of ignition delay

A novel in-cylinder pressure method for determining ignition delay has been proposed and demonstrated. This method proposes a new Bayesian statistical model to resolve the start of combustion, defined as being the point at which the band-pass in-cylinder pressure deviates from background noise and the combustion resonance begins. Further, it is demonstrated that this method is still accurate in situations where there is noise present. The start of combustion can be resolved for each cycle without the need for ad hoc methods such as cycle averaging. Therefore, this method allows for analysis of consecutive cycles and inter-cycle variability studies. Ignition delay obtained by this method and by the net rate of heat release have been shown to give good agreement. However, the use of combustion resonance to determine the start of combustion is preferable over the net rate of heat release method because it does not rely on knowledge of heat losses and will still function accurately in the presence of noise. Results for a six-cylinder turbo-charged common-rail diesel engine run with neat diesel fuel at full, three quarters and half load have been presented. Under these conditions the ignition delay was shown to increase as the load was decreased with a significant increase in ignition delay at half load, when compared with three quarter and full loads.

The Tashi project 2004-2010 : developing methods for creating theatre works that fully engage children aged between 3 and 10

Over a seven-year period, Mark Radvan directed a suite of children’s theatre productions adapted from the original Tashi stories by Australian writers Anna and Barbara Fienberg. The Tashi Project’s repertoire of plays performed to over 40,000 children aged between 3 and 10 years old, and their carers, in seasons at the Out of the Box Festival, at Brisbane Powerhouse and in venues across Australia in two interstate tours in 2009 and 2010. The project investigated how best to combine an exploration of theatrical forms and conventions, with a performance style evolved in a specially developed training program and a deliberate positioning of young children as audiences capable of sophisticated readings of action, symbol, theme and character. The results of this project show that when brought into appropriate relationship with the theatre artists, young children aged 3-5 can engage with sophisticated narrative forms, and with the right contextual framing they enjoy heightened dramatic and emotional tension, bringing to the event sustained and highly engaged concentration. Older children aged 6-10 also bring sustained and heightened engagement to the same stories, providing that other more sophisticated dramatic elements are woven into the construction of the performances, such as character, theme and style.

The use of electronic portal imaging to verify patient position during intensity-modulated radiotherapy delivered by the dynamic MLC technique

Purpose: The precise shape of the three-dimensional dose distributions created by intensity-modulated radiotherapy means that the verification of patient position and setup is crucial to the outcome of the treatment. In this paper, we investigate and compare the use of two different image calibration procedures that allow extraction of patient anatomy from measured electronic portal images of intensity-modulated treatment beams. Methods and Materials: Electronic portal images of the intensity-modulated treatment beam delivered using the dynamic multileaf collimator technique were acquired. The images were formed by measuring a series of frames or segments throughout the delivery of the beams. The frames were then summed to produce an integrated portal image of the delivered beam. Two different methods for calibrating the integrated image were investigated with the aim of removing the intensity modulations of the beam. The first involved a simple point-by-point division of the integrated image by a single calibration image of the intensity-modulated beam delivered to a homogeneous polymethyl methacrylate (PMMA) phantom. The second calibration method is known as the quadratic calibration method and required a series of calibration images of the intensity-modulated beam delivered to different thicknesses of homogeneous PMMA blocks. Measurements were made using two different detector systems: a Varian amorphous silicon flat-panel imager and a Theraview camera-based system. The methods were tested first using a contrast phantom before images were acquired of intensity-modulated radiotherapy treatment delivered to the prostate and pelvic nodes of cancer patients at the Royal Marsden Hospital. Results: The results indicate that the calibration methods can be used to remove the intensity modulations of the beam, making it possible to see the outlines of bony anatomy that could be used for patient position verification. This was shown for both posterior and lateral delivered fields. Conclusions: Very little difference between the two calibration methods was observed, so the simpler division method, requiring only the single extra calibration measurement and much simpler computation, was the favored method. This new method could provide a complementary tool to existing position verification methods, and it has the advantage that it is completely passive, requiring no further dose to the patient and using only the treatment fields.

The influence of temperature and introduction point on the detection of Rhyzopertha dominica in stored grain

The presence of insect pests in grain storages throughout the supply chain is a significant problem for farmers, grain handlers, and distributors world-wide. Insect monitoring and sampling programmes are used in the stored grains industry for the detection and estimation of pest populations. At the low pest densities dictated by economic and commercial requirements, the accuracy of both detection and abundance estimates can be influenced by variations in the spatial structure of pest populations over short distances. Geostatistical analysis of Rhyzopertha dominica populations in 2 and 3 dimensions showed that insect numbers were positively correlated over short (0.5 cm) distances, and negatively correlated over longer (.10 cm) distances. At 35 C, insects were located significantly further from the grain surface than at 25 and 30 C. Dispersion metrics showed statistically significant aggregation in all cases. The observed heterogeneous spatial distribution of R. dominica may also be influenced by factors such as the site of initial infestation and disturbance during handling. To account for these additional factors, I significantly extended a simulation model that incorporates both pest growth and movement through a typical stored-grain supply chain. By incorporating the effects of abundance, initial infestation site, grain handling, and treatment on pest spatial distribution, I developed a supply chain model incorporating estimates of pest spatial distribution. This was used to examine several scenarios representative of grain movement through a supply chain, and determine the influence of infestation location and grain disturbance on the sampling intensity required to detect pest infestations at various infestation rates. This study has investigated the effects of temperature, infestation point, and grain handling on the spatial distribution and detection of R. dominica. The proportion of grain infested was found to be dependent upon abundance, initial pest location, and grain handling. Simulation modelling indicated that accounting for these factors when developing sampling strategies for stored grain has the potential to significantly reduce sampling costs while simultaneously improving detection rate, resulting in reduced storage and pest management cost while improving grain quality.

Nuclear instruments and methods in physics research section B : beam interactions with materials and atoms

The impact-induced deposition of Al13 clusters with icosahedral structure on Ni(0 0 1) surface was studied by molecular dynamics (MD) simulation using Finnis–Sinclair potentials. The incident kinetic energy (Ein) ranged from 0.01 to 30 eV per atom. The structural and dynamical properties of Al clusters on Ni surfaces were found to be strongly dependent on the impact energy. At much lower energy, the Al cluster deposited on the surface as a bulk molecule. However, the original icosahedral structure was transformed to the fcc-like one due to the interaction and the structure mismatch between the Al cluster and Ni surface. With increasing the impinging energy, the cluster was deformed severely when it contacted the substrate, and then broken up due to dense collision cascade. The cluster atoms spread on the surface at last. When the impact energy was higher than 11 eV, the defects, such as Al substitutions and Ni ejections, were observed. The simulation indicated that there exists an optimum energy range, which is suitable for Al epitaxial growth in layer by layer. In addition, at higher impinging energy, the atomic exchange between Al and Ni atoms will be favourable to surface alloying.