Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

Algebraic attacks on clock-controlled stream ciphers

Stream ciphers are encryption algorithms used for ensuring the privacy of digital telecommunications. They have been widely used for encrypting military communications, satellite communications, pay TV encryption and for voice encryption of both fixed lined and wireless networks. The current multi year European project eSTREAM, which aims to select stream ciphers suitable for widespread adoptation, reflects the importance of this area of research. Stream ciphers consist of a keystream generator and an output function. Keystream generators produce a sequence that appears to be random, which is combined with the plaintext message using the output function. Most commonly, the output function is binary addition modulo two. Cryptanalysis of these ciphers focuses largely on analysis of the keystream generators and of relationships between the generator and the keystream it produces. Linear feedback shift registers are widely used components in building keystream generators, as the sequences they produce are well understood. Many types of attack have been proposed for breaking various LFSR based stream ciphers. A recent attack type is known as an algebraic attack. Algebraic attacks transform the problem of recovering the key into a problem of solving multivariate system of equations, which eventually recover the internal state bits or the key bits. This type of attack has been shown to be effective on a number of regularly clocked LFSR based stream ciphers. In this thesis, algebraic attacks are extended to a number of well known stream ciphers where at least one LFSR in the system is irregularly clocked. Applying algebriac attacks to these ciphers has only been discussed previously in the open literature for LILI-128. In this thesis, algebraic attacks are first applied to keystream generators using stop-and go clocking. Four ciphers belonging to this group are investigated: the Beth-Piper stop-and-go generator, the alternating step generator, the Gollmann cascade generator and the eSTREAM candidate: the Pomaranch cipher. It is shown that algebraic attacks are very effective on the first three of these ciphers. Although no effective algebraic attack was found for Pomaranch, the algebraic analysis lead to some interesting findings including weaknesses that may be exploited in future attacks. Algebraic attacks are then applied to keystream generators using (p; q) clocking. Two well known examples of such ciphers, the step1/step2 generator and the self decimated generator are investigated. Algebraic attacks are shown to be very powerful attack in recovering the internal state of these generators. A more complex clocking mechanism than either stop-and-go or the (p; q) clocking keystream generators is known as mutual clock control. In mutual clock control generators, the LFSRs control the clocking of each other. Four well known stream ciphers belonging to this group are investigated with respect to algebraic attacks: the Bilateral-stop-and-go generator, A5/1 stream cipher, Alpha 1 stream cipher, and the more recent eSTREAM proposal, the MICKEY stream ciphers. Some theoretical results with regards to the complexity of algebraic attacks on these ciphers are presented. The algebraic analysis of these ciphers showed that generally, it is hard to generate the system of equations required for an algebraic attack on these ciphers. As the algebraic attack could not be applied directly on these ciphers, a different approach was used, namely guessing some bits of the internal state, in order to reduce the degree of the equations. Finally, an algebraic attack on Alpha 1 that requires only 128 bits of keystream to recover the 128 internal state bits is presented. An essential process associated with stream cipher proposals is key initialization. Many recently proposed stream ciphers use an algorithm to initialize the large internal state with a smaller key and possibly publicly known initialization vectors. The effect of key initialization on the performance of algebraic attacks is also investigated in this thesis. The relationships between the two have not been investigated before in the open literature. The investigation is conducted on Trivium and Grain-128, two eSTREAM ciphers. It is shown that the key initialization process has an effect on the success of algebraic attacks, unlike other conventional attacks. In particular, the key initialization process allows an attacker to firstly generate a small number of equations of low degree and then perform an algebraic attack using multiple keystreams. The effect of the number of iterations performed during key initialization is investigated. It is shown that both the number of iterations and the maximum number of initialization vectors to be used with one key should be carefully chosen. Some experimental results on Trivium and Grain-128 are then presented. Finally, the security with respect to algebraic attacks of the well known LILI family of stream ciphers, including the unbroken LILI-II, is investigated. These are irregularly clock- controlled nonlinear filtered generators. While the structure is defined for the LILI family, a particular paramater choice defines a specific instance. Two well known such instances are LILI-128 and LILI-II. The security of these and other instances is investigated to identify which instances are vulnerable to algebraic attacks. The feasibility of recovering the key bits using algebraic attacks is then investigated for both LILI- 128 and LILI-II. Algebraic attacks which recover the internal state with less effort than exhaustive key search are possible for LILI-128 but not for LILI-II. Given the internal state at some point in time, the feasibility of recovering the key bits is also investigated, showing that the parameters used in the key initialization process, if poorly chosen, can lead to a key recovery using algebraic attacks.

Gene transfer to plants by diverse species of bacteria

Agrobacterium is widely considered to be the only bacterial genus capable of transferring genes to plants. When suitably modified, Agrobacterium has become the most effective vector for gene transfer in plant biotechnology1. However, the complexity of the patent landscape2 has created both real and perceived obstacles to the effective use of this technology for agricultural improvements by many public and private organizations worldwide. Here we show that several species of bacteria outside the Agrobacterium genus can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria were made competent for gene transfer by acquisition of both a disarmed Ti plasmid and a suitable binary vector. This alternative to Agrobacterium-mediated technology for crop improvement, in addition to affording a versatile ‘open source’ platform for plant biotechnology, may lead to new uses of natural bacteria– plant interactions to achieve plant transformation.

The first Australian nurse practitioner census : a protocol to guide standardized collection of information about an emergent professional group

Internationally, collection of reliable data on new and evolving health-care roles is crucial. We describe a protocol for design and administration of a national census of an emergent health-care role, namely nurse practitioners in Australia using databases held by regulatory authorities. A questionnaire was developed to obtain data on the role and scope of practice of Australian nurse practitioners. Our tool comprised five sections and included a total of 56 questions, using 28 existing items from the National Nursing and Midwifery Labour Force Census and nine items recommended in the Nurse Practitioner Workforce Planning Minimum Data Set. Australian Nurse Registering Authorities (n = 6) distributed the survey on our behalf. This paper outlines our instrument and methods. The survey was administered to 238 authorized Australian nurse practitioners (85% response rate). Rigorous collection of standardized items will ensure health policy is informed by reliable and valid data. We will re-administer the survey 2 years following the first survey to measure change over time.

The effectiveness of a short-term group music therapy intervention for parents who have a child with a disability

The relationship between the quality of parent-child interactions and positive child developmental trajectories is well established (Guralnick, 2006; Shonkoff & Meissels, 2000; Zubrick et al., 2008). However, a range of parental, family, and socio-economic factors can pose risks to parents’ capacity to participate in quality interactions with their children. In particular, families with a child with a disability have been found to have higher levels of parenting stress, and are more likely to experience economic disadvantage, as well as social isolation. The importance of early interventions to promote positive parenting and child development for these families is widely recognised (Shonkoff & Meissels, 2000). However, to date, there is a lack of evidence about the effectiveness of early parenting programs for families who have a young child with a disability. This thesis investigates the impact of a music therapy parenting program, Sing & Grow, on 201 parent-child dyads who attended programs specifically targeted to parents who had a young child with a disability. Sing & Grow is an Australian national early parenting intervention funded by the Australian Government Department of Families, Housing, Community Services and Indigenous Affairs and delivered by Playgroup Queensland. It is designed and delivered by Registered Music Therapists for families with children aged from birth to three years. It aims to improve parenting skills and confidence, improve family functioning (positive parent-child interactions), enhance child development, and provide social networking opportunities to socially isolated families. The intervention targets a range of families in circumstances that have the potential to impact negatively on family functioning. This thesis uses data from the National Evaluation Study of Sing & Grow from programs which were targeted at families who had a young child with a disability. Three studies were conducted to address the objectives of this thesis. Study 1 examines the effects of the Sing & Grow intervention on parent reported pre and post parent mental health, parenting confidence, parenting skills, and child development, and other parent reported outcomes including social support, use of intervention resources, satisfaction with the intervention and perceived benefits of and barriers to participation. Significant improvements from pre to post were found for parent mental health and parent reported child communication and social skills, along with evidence that parents were very satisfied with the program and that it brought social benefits to families. Study 2 explored the pre to post effects of the intervention on children’s developmental skills and parent-child interactions using observational ratings made by clinicians. Significant pre to post improvements were found for parenting sensitivity, parental engagement with child and acceptance of child as well as for child responsiveness to parent, interest, and participation in the intervention, and social skills. Study 3 examined the nature of child and family characteristics that predicted better outcomes for families while taking account of the level of participation in the program. An overall outcome index was calculated and served as the dependent variable in a logistic regression analysis. Families who attended six or more sessions and mothers who had not completed high school were more likely to have higher outcome scores at post intervention than those who attended fewer sessions and those with more educated mothers respectively. The findings of this research indicate that the intervention had a positive impact on participants’ mental health, parenting behaviours and child development and that level of attendance was associated with better outcomes. There was also evidence that the program reached its target of high risk families (i.e., families in which mothers had lower educational levels) and that for these families better outcomes were achieved. There were also indications that the program was accessible and highly regarded by families and that it promoted social connections for participants. A theoretical model of how the intervention is currently working for families is proposed to explain the connections between early parenting, child development and maternal wellbeing. However, more research is required to further elucidate the mechanisms by which the intervention creates change for families. This research presents promising evidence that a short term group music therapy program can elicit important therapeutic benefits for families who have a child with a disability.

Design and analysis of group key exchange protocols

A group key exchange (GKE) protocol allows a set of parties to agree upon a common secret session key over a public network. In this thesis, we focus on designing efficient GKE protocols using public key techniques and appropriately revising security models for GKE protocols. For the purpose of modelling and analysing the security of GKE protocols we apply the widely accepted computational complexity approach. The contributions of the thesis to the area of GKE protocols are manifold. We propose the first GKE protocol that requires only one round of communication and is proven secure in the standard model. Our protocol is generically constructed from a key encapsulation mechanism (KEM). We also suggest an efficient KEM from the literature, which satisfies the underlying security notion, to instantiate the generic protocol. We then concentrate on enhancing the security of one-round GKE protocols. A new model of security for forward secure GKE protocols is introduced and a generic one-round GKE protocol with forward security is then presented. The security of this protocol is also proven in the standard model. We also propose an efficient forward secure encryption scheme that can be used to instantiate the generic GKE protocol. Our next contributions are to the security models of GKE protocols. We observe that the analysis of GKE protocols has not been as extensive as that of two-party key exchange protocols. Particularly, the security attribute of key compromise impersonation (KCI) resilience has so far been ignored for GKE protocols. We model the security of GKE protocols addressing KCI attacks by both outsider and insider adversaries. We then show that a few existing protocols are not secure against KCI attacks. A new proof of security for an existing GKE protocol is given under the revised model assuming random oracles. Subsequently, we treat the security of GKE protocols in the universal composability (UC) framework. We present a new UC ideal functionality for GKE protocols capturing the security attribute of contributiveness. An existing protocol with minor revisions is then shown to realize our functionality in the random oracle model. Finally, we explore the possibility of constructing GKE protocols in the attribute-based setting. We introduce the concept of attribute-based group key exchange (AB-GKE). A security model for AB-GKE and a one-round AB-GKE protocol satisfying our security notion are presented. The protocol is generically constructed from a new cryptographic primitive called encapsulation policy attribute-based KEM (EP-AB-KEM), which we introduce in this thesis. We also present a new EP-AB-KEM with a proof of security assuming generic groups and random oracles. The EP-AB-KEM can be used to instantiate our generic AB-GKE protocol.

Quality of life after total laparoscopic hysterectomy versus total abdominal hysterectomy for stage I endometrial cancer (LACE) : a randomised trial

Background: The two-stage Total Laparoscopic Hysterectomy (TLH) versus Total Abdominal Hysterectomy (TAH) for stage I endometrial cancer (LACE) randomised controlled trial was initiated in 2005. The primary objective of stage 1 was to assess whether TLH results in equivalent or improved QoL up to 6 months after surgery compared to TAH. The primary objective of stage 2 was to test the hypothesis that disease-free survival at 4.5 years is equivalent for TLH and TAH. Results addressing the primary objective of stage 1 of the LACE trial are presented here. Methods: The first 361 LACE participants (TAH n= 142, TLH n=190) were enrolled in the QoL substudy at 19 centres across Australia, New Zealand and Hong Kong, and 332 completed the QoL analysis. Randomisation was performed centrally and independently from other study procedures via a computer generated, web-based system (providing concealment of the next assigned treatment) using stratified permuted blocks of 3 and 6, and assigned patients with histologically confirmed stage 1 endometrioid endometrial adenocarcinoma and ECOG performance status <2 to TLH or TAH stratified by histological grade and study centre. No blinding of patients or study personnel was attempted. QoL was measured at baseline, 1 and 4 weeks (early), and 3 and 6 months (late) after surgery using the Functional Assessment of Cancer Therapy-General (FACT-G) questionnaire. The primary endpoint was the difference between the groups in QoL change from baseline at early and late time points (a 5% difference was considered clinically significant). Analysis was performed according to the intention-to-treat principle using generalized estimating equations on differences from baseline for the early and late QoL recovery. The LACE trial is registered with clinicaltrials.gov (NCT00096408) and the Australian New Zealand Clinical Trials Registry (CTRN12606000261516). Patients for both stages of the trial have now been recruited and are being followed up for disease-specific outcomes. Findings: The proportion of missing values at the 5%, 10% 15% and 20% differences in the FACT-G scale was 6% (12/190) in the TLH and 14% (20/142) in the TAH group. There were 8/332 conversions (2.4%, 7 of which were from TLH to TAH). In the early phase of recovery, patients undergoing TLH reported significantly greater improvement of QoL from baseline compared to TAH in all subscales except the emotional and social well-being subscales. Improvements in QoL up to 6 months post-surgery continued to favour TLH except for the emotional and social well-being of the FACT and the visual analogue scale of the EuroQoL five dimensions (EuroQoL-VAS). Length of operating time was significantly longer in the TLH group (138±43 mins), than in the TAH group at (109±34 mins; p=0.001). While the proportion of intraoperative adverse events was similar between the treatment groups (TAH 8/142, 5.6%; TLH 14/190, 7.4%; p=0.55), postoperatively, twice as many patients in the TAH group experienced adverse events of CTC grade 3+ than in the TLH group (33/142, 23.2% and 22/190, 11.6%, respectively; p=0.004). Postoperative serious adverse events occurred more frequently in patients who had a TAH (27/142, 19.0%) than a TLH (15/190, 7.9%) (p=0.002). Interpretation: QoL improvements from baseline during early and later phases of recovery, and the adverse event profile significantly favour TLH compared to TAH for patients treated for Stage I endometrial cancer.

Some problems with a behavioristic account of early group pretense

In normal child development, both individual and group pretense first emerges at approximately two years of age. The metarepresentational account of pretense holds that children already have the concept PRETEND when they first engage in early group pretense. A behavioristic account suggests that early group pretense is analogous to early beliefs or desires and thus require no mental state concepts. I argue that a behavioral account does not explain the actual behavior observed in children and it cannot explain how children come to understand that a specific action is one of pretense versus one of belief. I conclude that a mentalistic explanation of pretense best explains the behavior under consideration.

Evaluation of the Scottsdale Loop 101 automated speed enforcement demonstration program

Speeding is recognized as a major contributing factor in traffic crashes. In order to reduce speed-related crashes, the city of Scottsdale, Arizona implemented the first fixed-camera photo speed enforcement program (SEP) on a limited access freeway in the US. The 9-month demonstration program spanning from January 2006 to October 2006 was implemented on a 6.5 mile urban freeway segment of Arizona State Route 101 running through Scottsdale. This paper presents the results of a comprehensive analysis of the impact of the SEP on speeding behavior, crashes, and the economic impact of crashes. The impact on speeding behavior was estimated using generalized least square estimation, in which the observed speeds and the speeding frequencies during the program period were compared to those during other periods. The impact of the SEP on crashes was estimated using 3 evaluation methods: a before-and-after (BA) analysis using a comparison group, a BA analysis with traffic flow correction, and an empirical Bayes BA analysis with time-variant safety. The analysis results reveal that speeding detection frequencies (speeds> or =76 mph) increased by a factor of 10.5 after the SEP was (temporarily) terminated. Average speeds in the enforcement zone were reduced by about 9 mph when the SEP was implemented, after accounting for the influence of traffic flow. All crash types were reduced except rear-end crashes, although the estimated magnitude of impact varies across estimation methods (and their corresponding assumptions). When considering Arizona-specific crash related injury costs, the SEP is estimated to yield about $17 million in annual safety benefits.

Group segmentation during object tracking using optical flow discontinuities

Within a surveillance video, occlusions are commonplace, and accurately resolving these occlusions is key when seeking to accurately track objects. The challenge of accurately segmenting objects is further complicated by the fact that within many real-world surveillance environments, the objects appear very similar. For example, footage of pedestrians in a city environment will consist of many people wearing dark suits. In this paper, we propose a novel technique to segment groups and resolve occlusions using optical flow discontinuities. We demonstrate that the ratio of continuous to discontinuous pixels within a region can be used to locate the overlapping edges, and incorporate this into an object tracking framework. Results on a portion of the ETISEO database show that the proposed algorithm results in improved tracking performance overall, and improved tracking within occlusions.

Civic engagement and associationalism : the impact of group membership scope versus intensity of participation

The relationship between participation in civic and political activities and membership of voluntary associations is now well established. What is less clear is the relative impacts of how much time people spend on group activities (associational intensity), and the number and type of groups that individuals are involved with (associational scope). Does it matter in terms of civic engagement, for example, whether one is a member of a quilting-circle or trade union? Does it matter whether association ‘membership’ is simply an annual payment or a major commitment of time and energy? In this article, we use a large survey to explore these questions empirically by focusing on the membership patterns and civic engagement practices of 4,001 citizens drawn from eight suburbs across Greater Melbourne, Australia. Our findings indicate that, while associational intensity is positively related to civic engagement, associational scope (the number of group memberships per person), is a more influential determinant of the level of civic and political participation. The results also suggest that while all forms of associationalism are important in terms of fostering greater levels of civic activity, not all forms have the same impact.

Optimism about safety and group-serving interpretations of safety among pedestrians and cyclists in relation to road use in general and under low light conditions

Drivers are known to be optimistic about their risk of crash involvement, believing that they are less likely to be involved in a crash than other drivers. However, little comparative research has been conducted among other road users. In addition, optimism about crash risk is conceptualised as applying only to an individual’s assessment of his or her personal risk of crash involvement. The possibility that the self-serving nature of optimism about safety might be generalised to the group-level as a cyclist or a pedestrian, i.e., becoming group-serving rather than self-serving, has been overlooked in relation to road safety. This study analysed a subset of data collected as part of a larger research project on the visibility of pedestrians, cyclists and road workers, focusing on a set of questionnaire items administered to 406 pedestrians, 838 cyclists and 622 drivers. The items related to safety in various scenarios involving drivers, pedestrians and cyclists, allowing predictions to be derived about group differences in agreement with items based on the assumption that the results would exhibit group-serving bias. Analysis of the responses indicated that specific hypotheses about group-serving interpretations of safety and responsibility were supported in 22 of the 26 comparisons. When the nine comparisons relevant to low lighting conditions were considered separately, seven were found to be supported. The findings of the research have implications for public education and for the likely acceptance of messages which are inconsistent with current assumptions and expectations of pedestrians and cyclists. They also suggest that research into group-serving interpretations of safety, even for temporary roles rather than enduring groups, could be fruitful. Further, there is an implication that gains in safety can be made by better educating road users about the limitations of their visibility and the ramifications of this for their own road safety, particularly in low light.