Exploring privacy for ubiquitous computing: Tools, methods and experiments

Ubiquitous computing is about making computers and computerized artefacts a pervasive part of our everyday lifes, bringing more and more activities into the realm of information. The computationalization, informationalization of everyday activities increases not only our reach, efficiency and capabilities but also the amount and kinds of data gathered about us and our activities. In this thesis, I explore how information systems can be constructed so that they handle this personal data in a reasonable manner. The thesis provides two kinds of results: on one hand, tools and methods for both the construction as well as the evaluation of ubiquitous and mobile systems---on the other hand an evaluation of the privacy aspects of a ubiquitous social awareness system. The work emphasises real-world experiments as the most important way to study privacy. Additionally, the state of current information systems as regards data protection is studied. The tools and methods in this thesis consist of three distinct contributions. An algorithm for locationing in cellular networks is proposed that does not require the location information to be revealed beyond the user's terminal. A prototyping platform for the creation of context-aware ubiquitous applications called ContextPhone is described and released as open source. Finally, a set of methodological findings for the use of smartphones in social scientific field research is reported. A central contribution of this thesis are the pragmatic tools that allow other researchers to carry out experiments. The evaluation of the ubiquitous social awareness application ContextContacts covers both the usage of the system in general as well as an analysis of privacy implications. The usage of the system is analyzed in the light of how users make inferences of others based on real-time contextual cues mediated by the system, based on several long-term field studies. The analysis of privacy implications draws together the social psychological theory of self-presentation and research in privacy for ubiquitous computing, deriving a set of design guidelines for such systems. The main findings from these studies can be summarized as follows: The fact that ubiquitous computing systems gather more data about users can be used to not only study the use of such systems in an effort to create better systems but in general to study phenomena previously unstudied, such as the dynamic change of social networks. Systems that let people create new ways of presenting themselves to others can be fun for the users---but the self-presentation requires several thoughtful design decisions that allow the manipulation of the image mediated by the system. Finally, the growing amount of computational resources available to the users can be used to allow them to use the data themselves, rather than just being passive subjects of data gathering.

Mechanistic Aspects of Shape Selection and Symmetry Breaking during Nanostructure Growth by Wet Chemical Methods

The control of shapes of nanocrystals is crucial for using them as building blocks for various applications. In this paper, we present a critical overview of the issues involved in shape-controlled synthesis of nanostructures. In particular, we focus on the mechanisms by which anisotropic structures of high-symmetry materials (fcc crystals, for instance) could be realized. Such structures require a symmetry-breaking mechanism to be operative that typically leads to selection of one of the facets/directions for growth over all the other symmetry-equivalent crystallographic facets. We show how this selection could arise for the growth of one-dimensional structures leading to ultrafine metal nanowires and for the case of two-dimensional nanostructures where the layer-by-layer growth takes place at low driving forces leading to plate-shaped structures. We illustrate morphology diagrams to predict the formation of two-dimensional structures during wet chemical synthesis. We show the generality of the method by extending it to predict the growth of plate-shaped inorganics produced by a precipitation reaction. Finally, we present the growth of crystals under high driving forces that can lead to the formation of porous structures with large surface areas.

Generalised quaternion methods in conformal geometry

A new approach to Penrose's twistor algebra is given. It is based on the use of a generalised quaternion algebra for the translation of statements in projective five-space into equivalent statements in twistor (conformal spinor) space. The formalism leads toSO(4, 2)-covariant formulations of the Pauli-Kofink and Fierz relations among Dirac bilinears, and generalisations of these relations.

Statistical methods for analysis of multi-harvest data from perennial pasture variety selection trials

Variety selection in perennial pasture crops involves identifying best varieties from data collected from multiple harvest times in field trials. For accurate selection, the statistical methods for analysing such data need to account for the spatial and temporal correlation typically present. This paper provides an approach for analysing multi-harvest data from variety selection trials in which there may be a large number of harvest times. Methods are presented for modelling the variety by harvest effects while accounting for the spatial and temporal correlation between observations. These methods provide an improvement in model fit compared to separate analyses for each harvest, and provide insight into variety by harvest interactions. The approach is illustrated using two traits from a lucerne variety selection trial. The proposed method provides variety predictions allowing for the natural sources of variation and correlation in multi-harvest data.

Free/Open Source Software Development : Results and Research Methods

Free and open source software development is an alternative to traditional software engineering as an approach to the development of complex software systems. It is a way of developing software based on geographically distributed teams of volunteers without apparent central plan or traditional mechanisms of coordination. The purpose of this thesis is to summarize the current knowledge about free and open source software development and explore the ways on which further understanding on it could be gained. The results of research on the field as well as the research methods are introduced and discussed. Also adapting software process metrics to the context of free and open source software development is illustrated and the possibilities to utilize them as tools to validate other research are discussed.

Developing standardized methods to assess cost of healthy and unhealthy (current) diets in Australia

Unhealthy diets contribute at least 14% to Australia's disease burden and are driven by ‘obesogenic’ food environments. Compliance with dietary recommendations is particularly poor amongst disadvantaged populations including low socioeconomic groups, those living in rural/remote areas and Aboriginal and Torres Strait Islanders. The perception that healthy foods are expensive is a key barrier to healthy choices and a major determinant of diet-related health inequities. Available state/regional/local data (limited and non-comparable) suggests that, despite basic healthy foods not incurring GST, the cost of healthy food is higher and has increased more rapidly than unhealthy food over the last 15 years in Australia. However, there were no nationally standardised tools or protocols to benchmark, compare or monitor food prices and affordability in Australia. Globally, we are leading work to develop and test approaches to assess the price differential of healthy and less-healthy (current) diets under the food price module of the International Network for Food and Obesity/non-communicable diseases (NCDs) Research, Monitoring and Action Support (INFORMAS). This presentation describes contextualization of the INFORMAS approach to develop standardised Australian tools, survey protocols and data collection and analysis systems. The ‘healthy diet basket’ was based on the Australian Foundation Diet, 1 The ‘current diet basket’ and specific items included in each basket, were based on recent national dietary survey data.2 Data collection methods were piloted. The final tools and protocols were then applied to measure the price and affordability of healthy and less healthy (current) diets of different household groups in diverse communities across the nation. We have compared results for different geographical locations/population subgroups in Australia and assessed these against international INFORMAS benchmarks. The results inform the development of policy and practice, including those relevant to mooted changes to the GST base, to promote nutrition and healthy weight and prevent chronic disease in Australia.

Comparison of Prediction Based LSF Quantization Methods using Split VQ

Further improvement in performance, to achieve near transparent quality LSF quantization, is shown to be possible by using a higher order two dimensional (2-D) prediction in the coefficient domain. The prediction is performed in a closed-loop manner so that the LSF reconstruction error is the same as the quantization error of the prediction residual. We show that an optimum 2-D predictor, exploiting both inter-frame and intra-frame correlations, performs better than existing predictive methods. Computationally efficient split vector quantization technique is used to implement the proposed 2-D prediction based method. We show further improvement in performance by using weighted Euclidean distance.

Critical Discourse Analysis research methods for the English classroom

Critical Discourse Analysis (CDA) is an approach to analysing the discourses that operate in social contexts, such as classrooms in schools, and their material effects on people, such as teachers and learners. CDA offers a range of ways of engaging with the relationship between texts in context and the power they exercise. In this article, I overview key approaches and provide detail of Fairclough’s (1992, 2003) textually-oriented, linguistic method of CDA, with an example from my own research. I offer a challenge for English teachers, as researchers, to ‘make strange’ the familiar world of their classroom work, and in so doing, identify possibilities for productive change.

The doctrinal method: Incorporating interdisciplinary methods in reforming the law

The doctrinal methodology is in a period of change and transition. Realising that the scope of the doctrinal method is too constricting, academic lawyers are becoming eclectic in their use of research method. In this transitional time, legal scholars are increasingly infusing evidence (and methods) from other disciplines into their reasoning to bolster their reform recommendations. This article considers three examples of the interplay of the discipline of law with other disciplines in the pursuit of law reform. Firstly the article reviews studies on the extent of methodologies and reformist frameworks in PhD research in Australia. Secondly it analyses a ‘snapshot’ of recently published Australian journal articles on criminal law reform. Thirdly, it focuses on the law reform commissions, those independent government committees that play such an important role in law reform in common law jurisdictions. This examination demonstrates that while the doctrinal core of legal scholarship remains intact, legal scholars are endeavouring to accommodate statistics, comparative perspectives, social science evidence and methods, and theoretical analysis, within the legal research framework, in order to provide additional ballast to the recommendations for reform.

Evaluation of methods and applications for behavioural profiling of transgenic mice

During the last 10-15 years interest in mouse behavioural analysis has evolved considerably. The driving force is development in molecular biological techniques that allow manipulation of the mouse genome by changing the expression of genes. Therefore, with some limitations it is possible to study how genes participate in regulation of physiological functions and to create models explaining genetic contribution to various pathological conditions. The first aim of our study was to establish a framework for behavioural phenotyping of genetically modified mice. We established comprehensive battery of tests for the initial screening of mutant mice. These included tests for exploratory and locomotor activity, emotional behaviour, sensory functions, and cognitive performance. Our interest was in the behavioural patterns of common background strains used for genetic manipulations in mice. Additionally we studied the behavioural effect of sex differences, test history, and individual housing. Our findings highlight the importance of careful consideration of genetic background for analysis of mutant mice. It was evident that some backgrounds may mask or modify the behavioural phenotype of mutants and thereby lead to false positive or negative findings. Moreover, there is no universal strain that is equally suitable for all tests, and using different backgrounds allows one to address possible phenotype modifying factors. We discovered that previous experience affected performance in several tasks. The most sensitive traits were the exploratory and emotional behaviour, as well as motor and nociceptive functions. Therefore, it may be essential to repeat some of the tests in naïve animals for assuring the phenotype. Social isolation for a long time period had strong effects on exploratory behaviour, but also on learning and memory. All experiments revealed significant interactions between strain and environmental factors (test history or housing condition) indicating genotype-dependent effects of environmental manipulations. Several mutant line analyses utilize this information. For example, we studied mice overexpressing as well as those lacking extracellular matrix protein heparin-binding growth-associated molecule (HB-GAM), and mice lacking N-syndecan (a receptor for HB-GAM). All mutant mice appeared to be fertile and healthy, without any apparent neurological or sensory defects. The lack of HB-GAM and N-syndecan, however, significantly reduced the learning capacity of the mice. On the other hand, overexpression of HB-GAM resulted in facilitated learning. Moreover, HB-GAM knockout mice displayed higher anxiety-like behaviour, whereas anxiety was reduced in HB-GAM overexpressing mice. Changes in hippocampal plasticity accompanied the behavioural phenotypes. We conclude that HB-GAM and N-syndecan are involved in the modulation of synaptic plasticity in hippocampus and play a role in regulation of anxiety- and learning-related behaviour.

Computational methods for the prediction of the structure and interactions of coiled-coil peptides

The past several years have seen significant advances in the development of computational methods for the prediction of the structure and interactions of coiled-coil peptides. These methods are generally based on pairwise correlations of amino acids, helical propensity, thermal melts and the energetics of sidechain interactions, as well as statistical patterns based on Hidden Markov Model (HMM) and Support Vector Machine (SVM) techniques. These methods are complemented by a number of public databases that contain sequences, motifs, domains and other details of coiled-coil structures identified by various algorithms. Some of these computational methods have been developed to make predictions of coiled-coil structure on the basis of sequence information; however, structural predictions of the oligomerisation state of these peptides still remains largely an open question due to the dynamic behaviour of these molecules. This review focuses on existing in silico methods for the prediction of coiled-coil peptides of functional importance using sequence and/or three-dimensional structural data.

Application of optimization methods to vibration control of stretched strings

In this paper, non-linear programming techniques are applied to the problem of controlling the vibration pattern of a stretched string. First, the problem of finding the magnitudes of two control forces applied at two points l1 and l2 on the string to reduce the energy of vibration over the interval (l1, l2) relative to the energy outside the interval (l1, l2) is considered. For this problem the relative merits of various methods of non-linear programming are compared. The more complicated problem of finding the positions and magnitudes of two control forces to obtain the desired energy pattern is then solved by using the slack unconstrained minimization technique with the Fletcher-Powell search. In the discussion of the results it is shown that the position of the control force is very important in controlling the energy pattern of the string.

Microbial diversity in the municipal composting process and development of detection methods

Composting refers to aerobic degradation of organic material and is one of the main waste treatment methods used in Finland for treating separated organic waste. The composting process allows converting organic waste to a humus-like end product which can be used to increase the organic matter in agricultural soils, in gardening, or in landscaping. Microbes play a key role as degraders during the composting-process, and the microbiology of composting has been studied for decades, but there are still open questions regarding the microbiota in industrial composting processes. It is known that with the traditional, culturing-based methods only a small fraction, below 1%, of the species in a sample is normally detected. In recent years an immense diversity of bacteria, fungi and archaea has been found to occupy many different environments. Therefore the methods of characterising microbes constantly need to be developed further. In this thesis the presence of fungi and bacteria in full-scale and pilot-scale composting processes was characterised with cloning and sequencing. Several clone libraries were constructed and altogether nearly 6000 clones were sequenced. The microbial communities detected in this study were found to differ from the compost microbes observed in previous research with cultivation based methods or with molecular methods from processes of smaller scale, although there were similarities as well. The bacterial diversity was high. Based on the non-parametric coverage estimations, the number of bacterial operational taxonomic units (OTU) in certain stages of composting was over 500. Sequences similar to Lactobacillus and Acetobacteria were frequently detected in the early stages of drum composting. In tunnel stages of composting the bacterial community comprised of Bacillus, Thermoactinomyces, Actinobacteria and Lactobacillus. The fungal diversity was found to be high and phylotypes similar to yeasts were abundantly found in the full-scale drum and tunnel processes. In addition to phylotypes similar to Candida, Pichia and Geotrichum moulds from genus Thermomyces and Penicillium were observed in tunnel stages of composting. Zygomycetes were detected in the pilot-scale composting processes and in the compost piles. In some of the samples there were a few abundant phylotypes present in the clone libraries that masked the rare ones. The rare phylotypes were of interest and a method for collecting them from clone libraries for sequencing was developed. With negative selection of the abundant phylotyps the rare ones were picked from the clone libraries. Thus 41% of the clones in the studied clone libraries were sequenced. Since microbes play a central role in composting and in many other biotechnological processes, rapid methods for characterization of microbial diversity would be of value, both scientifically and commercially. Current methods, however, lack sensitivity and specificity and are therefore under development. Microarrays have been used in microbial ecology for a decade to study the presence or absence of certain microbes of interest in a multiplex manner. The sequence database collected in this thesis was used as basis for probe design and microarray development. The enzyme assisted detection method, ligation-detection-reaction (LDR) based microarray, was adapted for species-level detection of microbes characteristic of each stage of the composting process. With the use of a specially designed control probe it was established that a species specific probe can detect target DNA representing as little as 0.04% of total DNA in a sample. The developed microarray can be used to monitor composting processes or the hygienisation of the compost end product. A large compost microbe sequence dataset was collected and analysed in this thesis. The results provide valuable information on microbial community composition during industrial scale composting processes. The microarray method was developed based on the sequence database collected in this study. The method can be utilised in following the fate of interesting microbes during composting process in an extremely sensitive and specific manner. The platform for the microarray is universal and the method can easily be adapted for studying microbes from environments other than compost.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.