Cell migration and proliferation on homogeneous and non-homogeneous domains : modelling on the scale of individuals and populations

Cell migration is a behaviour critical to many key biological effects, including wound healing, cancerous cell invasion and morphogenesis, the development of an organism from an embryo. However, given that each of these situations is distinctly different and cells are extremely complicated biological objects, interest lies in more basic experiments which seek to remove conflating factors and present a less complex environment within which cell migration can be experimentally examined. These include in vitro studies like the scratch assay or circle migration assay, and ex vivo studies like the colonisation of the hindgut by neural crest cells. The reduced complexity of these experiments also makes them much more enticing as problems to mathematically model, like done here. The primary goal of the mathematical models used in this thesis is to shed light on which cellular behaviours work to generate the travelling waves of invasion observed in these experiments, and to explore how variations in these behaviours can potentially predict differences in this invasive pattern which are experimentally observed when cell types or chemical environment are changed. Relevant literature has already identified the difficulty of distinguishing between these behaviours when using traditional mathematical biology techniques operating on a macroscopic scale, and so here a sophisticated individual-cell-level model, an extension of the Cellular Potts Model (CPM), is been constructed and used to model a scratch assay experiment. This model includes a novel mechanism for dealing with cell proliferations that allowed for the differing properties of quiescent and proliferative cells to be implemented into their behaviour. This model is considered both for its predictive power and used to make comparisons with the travelling waves which result in more traditional macroscopic simulations. These comparisons demonstrate a surprising amount of agreement between the two modelling frameworks, and suggest further novel modifications to the CPM that would allow it to better model cell migration. Considerations of the model’s behaviour are used to argue that the dominant effect governing cell migration (random motility or signal-driven taxis) likely depends on the sort of invasion demonstrated by cells, as easily seen by microscopic photography. Additionally, a scratch assay simulated on a non-homogeneous domain consisting of a ’fast’ and ’slow’ region is also used to further differentiate between these different potential cell motility behaviours. A heterogeneous domain is a novel situation which has not been considered mathematically in this context, nor has it been constructed experimentally to the best of the candidate’s knowledge. Thus this problem serves as a thought experiment used to test the conclusions arising from the simulations on homogeneous domains, and to suggest what might be observed should this non-homogeneous assay situation be experimentally realised. Non-intuitive cell invasion patterns are predicted for diffusely-invading cells which respond to a cell-consumed signal or nutrient, contrasted with rather expected behaviour in the case of random-motility-driven invasion. The potential experimental observation of these behaviours is demonstrated by the individual-cell-level model used in this thesis, which does agree with the PDE model in predicting these unexpected invasion patterns. In the interest of examining such a case of a non-homogeneous domain experimentally, some brief suggestion is made as to how this could be achieved.

Robust image hash functions using higher order spectra

Robust hashing is an emerging field that can be used to hash certain data types in applications unsuitable for traditional cryptographic hashing methods. Traditional hashing functions have been used extensively for data/message integrity, data/message authentication, efficient file identification and password verification. These applications are possible because the hashing process is compressive, allowing for efficient comparisons in the hash domain but non-invertible meaning hashes can be used without revealing the original data. These techniques were developed with deterministic (non-changing) inputs such as files and passwords. For such data types a 1-bit or one character change can be significant, as a result the hashing process is sensitive to any change in the input. Unfortunately, there are certain applications where input data are not perfectly deterministic and minor changes cannot be avoided. Digital images and biometric features are two types of data where such changes exist but do not alter the meaning or appearance of the input. For such data types cryptographic hash functions cannot be usefully applied. In light of this, robust hashing has been developed as an alternative to cryptographic hashing and is designed to be robust to minor changes in the input. Although similar in name, robust hashing is fundamentally different from cryptographic hashing. Current robust hashing techniques are not based on cryptographic methods, but instead on pattern recognition techniques. Modern robust hashing algorithms consist of feature extraction followed by a randomization stage that introduces non-invertibility and compression, followed by quantization and binary encoding to produce a binary hash output. In order to preserve robustness of the extracted features, most randomization methods are linear and this is detrimental to the security aspects required of hash functions. Furthermore, the quantization and encoding stages used to binarize real-valued features requires the learning of appropriate quantization thresholds. How these thresholds are learnt has an important effect on hashing accuracy and the mere presence of such thresholds are a source of information leakage that can reduce hashing security. This dissertation outlines a systematic investigation of the quantization and encoding stages of robust hash functions. While existing literature has focused on the importance of quantization scheme, this research is the first to emphasise the importance of the quantizer training on both hashing accuracy and hashing security. The quantizer training process is presented in a statistical framework which allows a theoretical analysis of the effects of quantizer training on hashing performance. This is experimentally verified using a number of baseline robust image hashing algorithms over a large database of real world images. This dissertation also proposes a new randomization method for robust image hashing based on Higher Order Spectra (HOS) and Radon projections. The method is non-linear and this is an essential requirement for non-invertibility. The method is also designed to produce features more suited for quantization and encoding. The system can operate without the need for quantizer training, is more easily encoded and displays improved hashing performance when compared to existing robust image hashing algorithms. The dissertation also shows how the HOS method can be adapted to work with biometric features obtained from 2D and 3D face images.

Comparing and complementing methods : traditional market research vs. deep customer insights

Quantitative market data has traditionally been used throughout marketing and business as a tool to inform and direct design decisions. However, in our changing economic climate, businesses need to innovate and create products their customers will love. Deep customer insight methods move beyond just questioning customers and aims to provoke true emotional responses in order to reveal new opportunities that go beyond functional product requirements. This paper explores traditional market research methods and compares them to methods used to gain deep customer insights. This study reports on a collaborative research project with seven small to medium enterprises and four multi-national organisations. Firms were introduced to a design led innovation approach, and were taught the different methods to gain deep customer insights. Interviews were conducted to understand the experience and outcomes of pre-existing research methods and deep customer insight approaches. Findings concluded that deep customer insights were unlikely to be revealed through traditional market research techniques. The theoretical outcome of this study is a complementary methods matrix, providing guidance on appropriate research methods in accordance to a project’s timeline.

Social Media Sites as Online Information Grounds : An exploratory study of the ways in which Information Technology (IT) professionals experience social media

Social media tools are often the result of innovations in Information Technology and developed by IT professionals and innovators. Nevertheless, IT professionals, many of whom are responsible for designing and building social media technologies, have not been investigated on how they themselves use or experience social media for professional purposes. This study will use Information Grounds Theory (Pettigrew, 1998) as a framework to study IT professionals’ experience in using social media for professional purposes. Information grounds facilitates the opportunistic discovery of information within social settings created temporarily at a place where people gather for a specific purpose (e.g., doctors’ waiting rooms, office tea rooms etc.), but the social atmosphere stimulates spontaneous sharing of information (Pettigrew, 1999). This study proposes that social media has the qualities that make it a rich information grounds; people participate from separate “places” in cyberspace in a synchronous manner in real-time, making it almost as dynamic and unplanned as physical information grounds. There is limited research on how social media platforms are perceived as a “place,” (a place to go to, a place to gather, or a place to be seen in) that is comparable to physical spaces. There is also no empirical study on how IT professionals use or “experience” social media. The data for this study is being collected through a study of IT professionals who currently use Twitter. A digital ethnography approach is being taken wherein the researcher uses online observations and “follows” the participants online and observes their behaviours and interactions on social media. Next, a sub-set of participants will be interviewed on their experiences with and within social media and how social media compares with traditional methods of information grounds, information communication, and collaborative environments. An Evolved Grounded Theory (Glaser, 1992) approach will be used to analyse tweets data and interviews and to map the findings against the Information Ground Theory. Findings from this study will provide foundational understanding of IT professionals’ experiences within social media, and can help both professionals and researchers understand this fast-evolving method of communications.

Moving beyond traditional clinics : creating a new legal clinics through community partnerships

To overcome the challenge of finding placements for large student numbers, QUT has partnered with community organisations to enable students to work on community-based projects addressing a community need. Students work in interdisciplinary teams with the community organisation to resolve issues and identify solutions to suit the organisation and client base. This paper will describe the community engaged learning pedagogy that is employed in the subject and will consider the benefits and challenges to law students of working collaboratively and developing community relationships. Critical appraisal of the legal system and the role of lawyers and analysis of the professional and ethical responsibilities legal practitioners is a focus of the subject. Explicit emphasis is placed on developing a sense of social responsibility and inculcating a pro bono ethos. Students attend workshops on topics such as reflective practice, cultural competencies, client solutions, collaborative practice and ethical obligations. This paper will discuss the challenges in creating the new legal clinic subject, benefits to students and community partners, and the results of initial student evaluation of the subject.

A discourse on the non-method

In spite of the activism of professional bodies and researchers, empirical evidence shows that project management still does not deliver the expected benefits and promises. Hence, many have questioned the validity of the hegemonic rationalist paradigm anchored in the Enlightenment and Natural Sciences tradition supporting project management research and practice for the last 60 years and the lack of relevance to practice of the current conceptual base of project management. In order to address these limitations many authors, taking a post-modernist stance in social sciences, build on ‘pre-modern’ philosophies such as the Aristotelian one, specially emphasizing the role of praxis (activity), and phronesis (practical wisdom, prudence). Indeed, ‘Praxis … is the central category of the philosophy which is not merely an interpretation of the world, but is also a guide to its transformation …’ (Vazquez, 1977:. 149). Therefore, praxis offers an important focus for practitioners and researchers in social sciences, one in which theory is integrated with practice at the point of intervention. Simply stated, praxis can serve as a common ground for those interested in basic and applied research by providing knowledge of the reality in which action, informed by theory, takes place. Consequently, I suggest a ‘praxeological’ style of reasoning (praxeology being defined as study or science of human actions and conduct, including praxis, practices and phronesis) and to go beyond the ‘Theory-Practice’ divide. Moreover, I argue that we need to move away from the current dichotomy between the two classes ‘scholars experts-researchers’ and ‘managers/workers-practitioners-participants’. Considering one single class of ‘PraXitioner’, becoming a phronimos, may contribute to create new perspectives and open up new ways of thinking and acting in project situations. Thus, I call for a Perestroika in researching and acting in project management situations. My intent is to suggest a balanced praxeological view of the apparent opposition between social and natural science approaches. I explore, in this chapter, three key questions, covering the ontological, epistemological and praxeological dimensions of project management in action. 1. Are the research approaches being currently used appropriate for generating contributions that matter to both theory and practice with regards to what a ‘project’ is or to what we do when we call a specific situation ‘a project’? 2. On the basis of which intellectual virtues is the knowledge generated and what is the impact for theory and practice? 3. Are the modes of action of the practitioners ‘prudent’ and are they differentiating or reconciling formal and abstract rationality from substantive rationality and situated reasoning with regards to the mode of action they adopt in particular project situations? The investigation of the above questions leads me to debate about ‘Project Management-as-Praxis’, and to suggest ‘A’ (not ‘THE’) ‘praxeological’ style of reasoning and mode of inquiry – acknowledging a non-paradigmatic, subjective and kaleidoscopic perspective – for ‘Knowing-as-Practicing’ in project management. In short, this is about making a ‘Projects Science’ that matters.

A method for predicting rain-induced instability of an individual slope

Awareness to avoid losses and casualties due to rain-induced landslide is increasing in regions that routinely experience heavy rainfall. Improvements in early warning systems against rain-induced landslide such as prediction modelling using rainfall records, is urgently needed in vulnerable regions. The existing warning systems have been applied using stability chart development and real-time displacement measurement on slope surfaces. However, there are still some drawbacks such as: ignorance of rain-induced instability mechanism, mislead prediction due to the probabilistic prediction and short time for evacuation. In this research, a real-time predictive method was proposed to alleviate the drawbacks mentioned above. A case-study soil slope in Indonesia that failed in 2010 during rainfall was used to verify the proposed predictive method. Using the results from the field and laboratory characterizations, numerical analyses can be applied to develop a model of unsaturated residual soils slope with deep cracks and subject to rainwater infiltration. Real-time rainfall measurement in the slope and the prediction of future rainfall are needed. By coupling transient seepage and stability analysis, the variation of safety factor of the slope with time were provided as a basis to develop method for the real-time prediction of the rain-induced instability of slopes. This study shows the proposed prediction method has the potential to be used in an early warning system against landslide hazard, since the FOS value and the timing of the end-result of the prediction can be provided before the actual failure of the case study slope.

Integration of Saudi Arabia’s conservative Islamic culture in sustainable housing design

The cities of Saudi Arabia have perhaps the largest growth rates of cities in the Middle East, such that it has become a cause in shortage of housing for mid and low-income families, as is the case in other developing countries. Even when housing is found, it is not sustainable nor is it providing the cultural needs of those families. The aim of this paper is to integrate the unique conservative Islamic Saudi culture into the design of sustainable housing. This paper is part of a preliminary study of an on-going PhD thesis, which utilises a semistructured interview of a panel of nine experts in collecting the data. The interviews consisted of ten questions ranging from general questions such as stating their expertise and work position to more specific question such as listing the critical success factors and/or barriers for applying sustainability to housing in Saudi Arabia. Since the participants were selected according to their experience, the answers to the interview questions were satisfactory where the generation of the survey questions for the second stage in the PhD thesis took place after analysing the participant’s answers to the interview questions. This paper recommends design requirements for accommodating the conservative Islamic Saudi Culture in low cost sustainable houses. Such requirements include achieving privacy through the use of various types of traditional Saudi architectural elements, such as the method of decorative screening of windows, called Mashrabiya, and having an inner courtyard where the house looks inward rather than outward. Other requirements include educating firms on how to design sustainable housing, educating the public on the advantages of sustainable housing and implementing new laws that enforce the utilisation of sustainable methods to housing construction. This paper contributes towards the body of knowledge by proposing initial findings on how to integrate the conservative Islamic culture of Saudi Arabia into the design of a sustainable house specifically for mid and low-income families. This contribution can be implemented on developing countries in the region that are faced with housing shortage for mid and low-income families.

A data mining driven crash risk profiling method for road asset management

This thesis takes a new data mining approach for analyzing road/crash data by developing models for the whole road network and generating a crash risk profile. Roads with an elevated crash risk due to road surface friction deficit are identified. The regression tree model, predicting road segment crash rate, is applied in a novel deployment coined regression tree extrapolation that produces a skid resistance/crash rate curve. Using extrapolation allows the method to be applied across the network and cope with the high proportion of missing road surface friction values. This risk profiling method can be applied in other domains.

Encapsulation of transition metal species into zeolites and molecular sieves as redox catalysts: Part I-preparation and characterisation of nanosized TiO2, CdO and ZnO semiconductor particles anchored in NaY zeolite

In this paper, we report the preparation and characterisation of nanometer-sized TiO2, CdO, and ZnO semiconductor particles trapped in zeolite NaY. Preparation of these particles was carried out via the traditional ion exchange method and subsequent calcination procedure. It was found that the smaller cations, i.e., Cd2+ and Zn2+ could be readily introduced into the SI′ and SII′ sites located in the sodalite cages, through ion exchange; while this is not the case for the larger Ti species, i.e., Ti monomer [TiO]2+ or dimer [Ti2O3]2+ which were predominantly dispersed on the external surface of zeolite NaY. The subsequent calcination procedure promoted these Ti species to migrate into the internal surface of the supercages. These semiconductor particles confined in NaY zeolite host exhibited a significant blue shift in the UV-VIS absorption spectra, in contrast to the respective bulk semiconductor materials, due to the quantum size effect (QSE). The particle sizes calculated from the UV-VIS optical absorption spectra using the effective mass approximation model are in good agreement with the atomic absorption data.

Evaluation of the Suchey-Brooks method for aging Australian Caucasian Populations using multislice Computed Tomography reconstructions of the Pubic Symphyseal Surface

Establishing age-at-death for skeletal remains is a vital component of forensic anthropology. The Suchey-Brooks (S-B) method of age estimation has been widely utilised since 1986 and relies on a visual assessment of the pubic symphyseal surface in comparison to a series of casts. Inter-population studies (Kimmerle et al., 2005; Djuric et al., 2007; Sakaue, 2006) demonstrate limitations of the S-B method, however, no assessment of this technique specific to Australian populations has been published. Aim: This investigation assessed the accuracy and applicability of the S-B method to an adult Australian Caucasian population by highlighting error rates associated with this technique. Methods: Computed tomography (CT) and contact scans of the S-B casts were performed; each geometrically modelled surface was extracted and quantified for reference purposes. A Queensland skeletal database for Caucasian remains aged 15 – 70 years was initiated at the Queensland Health Forensic and Scientific Services – Forensic Pathology Mortuary (n=350). Three-dimensional reconstruction of the bone surface using innovative volume visualisation protocols in Amira® and Rapidform® platforms was performed. Samples were allocated into 11 sub-sets of 5-year age intervals and changes associated with the surface geometry were quantified in relation to age, gender and asymmetry. Results: Preliminary results indicate that computational analysis was successfully applied to model morphological surface changes. Significant differences in observed versus actual ages were noted. Furthermore, initial morphological assessment demonstrates significant bilateral asymmetry of the pubic symphysis, which is unaccounted for in the S-B method. These results propose refinements to the S-B method, when applied to Australian casework. Conclusion: This investigation promises to transform anthropological analysis to be more quantitative and less invasive using CT imaging. The overarching goal contributes to improving skeletal identification and medico-legal death investigation in the coronial process by narrowing the range of age-at-death estimation in a biological profile.

A data mining driven risk profiling method for road asset management

Road surface skid resistance has been shown to have a strong relationship to road crash risk, however, applying the current method of using investigatory levels to identify crash prone roads is problematic as they may fail in identifying risky roads outside of the norm. The proposed method analyses a complex and formerly impenetrable volume of data from roads and crashes using data mining. This method rapidly identifies roads with elevated crash-rate, potentially due to skid resistance deficit, for investigation. A hypothetical skid resistance/crash risk curve is developed for each road segment, driven by the model deployed in a novel regression tree extrapolation method. The method potentially solves the problem of missing skid resistance values which occurs during network-wide crash analysis, and allows risk assessment of the major proportion of roads without skid resistance values.

Metabolic urinary profiling of alcohol hepatotoxicity and intervention effects of Yin Chen Hao Tang in rats using ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry

This paper was designed to study metabonomic characters of the hepatotoxicity induced by alcohol and the intervention effects of Yin Chen Hao Tang (YCHT), a classic traditional Chinese medicine formula for treatment of jaundice and liver disorders in China. Urinary samples from control, alcohol- and YCHT-treated rats were analyzed by ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) in positive ionization mode. The total ion chromatograms obtained from the control, alcohol- and YCHT-treated rats were easily distinguishable using a multivariate statistical analysis method such as the principal components analysis (PCA). The greatest difference in metabolic profiling was observed from alcohol-treated rats compared with the control and YCHT-treated rats. The positive ions m/z 664.3126 (9.00 min) was elevated in urine of alcohol-treated rats, whereas, ions m/z 155.3547 (10.96 min) and 708.2932 (9.01 min) were at a lower concentration compared with that in urine of control rats, however, these ions did not indicate a statistical difference between control rats and YCHT-treated rats. The ion m/z 664.3126 was found to correspond to ceramide (d18:1/25:0), providing further support for an involvement of the sphingomyelin signaling pathway in alcohol hepatotoxicity and the intervention effects of YCHT.

Simultaneous determination by UPLC-ESI-MS of scoparone, capillarisin, rhein, and emodin in rat urine after oral administration of Yin Chen Hao Tang preparation

A simple, sensitive, and validated method was developed for simultaneous determination of scoparone, capillarisin, rhein, and emodin in rat urine by ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC-MS). The urinary samples were analyzed on an Acquity UPLC BEH C18 1.7 microm 2.1x50 mm column. Scoparone, capillarisin, rhein, and emodin in rat urine were simultaneously analyzed with good separation. The lower limits of detection were 6.0, 9.0, 7.0, and 3.0 ng/mL, and the lower limits of quantification were 20.0, 33.0, 24.0, and 12.0 ng/mL for scoparone, capillarisin, rhein, and emodin, respectively. The intra- and inter-day precisions (RSD) were less than 9%. The intra- and inter-accuracies were found to be in the range of 94.14-104.54% for scoparone, 101.72-107.34% for capillarisin, 95.24-103.59% for rhein, and 101.32-107.82% for emodin at three concentration levels. The absolute recoveries for scoparone, capillarisin, rhein, and emodin were not less than 77.0%. The developed method has been applied to determine scoparone, capillarisin, rhein, and emodin in rat urine after oral administration of Yin Chen Hao Tang preparation, a traditional Chinese medicine formulation widely used in China for treatment of jaundice and liver disorders.

Pharmacokinetic studies of a Chinese triple herbal drug formula

Yin Chen Hao Tang preparation (YCHTP) is a classic traditional Chinese medicine formula, which is commonly used for clinical treatment of hepatological diseases. In this study, a rapid and validated high-performance liquid chromatography (HPLC) method was developed to simultaneously identify 6,7-dimethylesculetin and geniposide in rat plasma. This assay was performed on a Dikma Diamonsil RP(18) column (200 mmx4.6 mm, 5 mum) with acetonitrile-methanol-water (0.1% formic acid) as the mobile phase, showing acceptable linearity, intra- and inter-day precision and accuracy (R.S.D.=5%), and absolute recovery for two analytes (74%); the limits of quantitation were 0.4 and 1.12 mug/ml, and the limits of detection were 0.06 and 0.09 mug/ml for two analytes. The developed method was successfully applied to study the effect of formula compatibility on the pharmacokinetics of 6,7-dimethylesculetin and geniposide in YCHTP when orally administrating an effective human daily dose of YCHTP to rats. We surmise that formula compatibility can significantly influence the pharmacokinetics of YCHTP, and we have elucidated and validated the compatible administration of YCHTP.