Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

Allegations of child sexual abuse in family court cases : a qualitative analysis of psychiatric evidence

Allegations of child sexual abuse in Family Court cases have gained increasing attention. The study investigates factors involved in Family Court cases involving allegations of child sexual abuse. A qualitative methodology was employed to examine Records of Judgement and Psychiatric Reports for 20 cases distilled from the data corpus of 102 cases. A seven-stage methodology was developed utilising a thematic analysis process informed by principles of grounded theory and phenomenology. The explication of eight thematic clusters was undertaken. The findings point to complex issues and dynamics in which child sexual abuse allegations have been raised. The alleging parent’s allegations of sexual abuse against their ex-partner may be: the expression of unconscious deep fears for their children’s welfare, or an action to meet their needs for personal affirmation in the context of the painful upheaval of a relationship break-up. Implications of the findings are discussed.

Network interactions and performance of a multi-function IEC 61850 process bus

New substation technology, such as non-conventional instrument transformers,and a need to reduce design and construction costs, are driving the adoption of Ethernet based digital process bus networks for high voltage substations. Protection and control applications can share a process bus, making more efficient use of the network infrastructure. This paper classifies and defines performance requirements for the protocols used in a process bus on the basis of application. These include GOOSE, SNMP and IEC 61850-9-2 sampled values. A method, based on the Multiple Spanning Tree Protocol (MSTP) and virtual local area networks, is presented that separates management and monitoring traffic from the rest of the process bus. A quantitative investigation of the interaction between various protocols used in a process bus is described. These tests also validate the effectiveness of the MSTP based traffic segregation method. While this paper focusses on a substation automation network, the results are applicable to other real-time industrial networks that implement multiple protocols. High volume sampled value data and time-critical circuit breaker tripping commands do not interact on a full duplex switched Ethernet network, even under very high network load conditions. This enables an efficient digital network to replace a large number of conventional analog connections between control rooms and high voltage switchyards.

Interactions and consequences of inertia and switching costs

Purpose: Service research typically relates switching costs to customer loyalty, and portrays them as effective switching deterrents that engender harmful word-of-mouth (WOM). Rather than to customer loyalty, this paper aims to relate switching costs to consumer inertia, and show that while switching costs may result in customer retention, they can engender positive and negative WOM. This depends on whether the inertia stems from satisfaction or indifference. Design/methodology/approach: A mall-intercept survey investigated 518 customers' perceptions of their mobile phone service providers. Structural equation modelling fitted the data to the conceptual model. Findings: Switching costs deterred switching and engendered negative WOM, but only with low-inertia customers. With high-inertia customers, retention and WOM behaviours depended on whether the inertia stemmed from satisfaction or indifference. Satisfied customers with high switching costs tended to stay, gave more positive and less negative WOM. With indifferent customers, switching costs were unrelated to retention or WOM behaviours. Research limitations/implications: While they may be perceived negatively, switching costs can engender PWOM. Hence, research should not consider switching costs alone without considering the context that produces them. Practical implications: Service providers should segment their customers into low-inertia, high-inertia/satisfied and high-inertia/indifferent, and target each segment differently. By converting customers into the high-inertia/satisfied segment, service providers can make the best use of switching costs – not only in the traditional sense as a barrier to defection, but also as a way of generating positive WOM. Originality/value: This study is the first to consider the role of inertia with switching costs, positive WOM, and negative WOM. The findings suggest that past studies portraying switching costs as negative impediments that evoke only negative WOM might be misleading.

Catapulting into STEM education : female students’ interactions within a middle school engineering project

Despite efforts to motivate students to engage in Science, technology, engineering and mathematics (STEM) education, women are still underrepresented in these areas in the workforce and higher education. Targeting females at high school or earlier may be a key towards engaging them in STEM. In this paper we report on the research question: How do middle school females interact for learning about engineering education? This ethnographic study, part of a three-year longitudinal research project, investigated Year 8 female students’ learning about engineering concepts associated with designing, constructing, testing, and evaluating a catapult. Through a series of lead-up lessons and the four lesson catapult challenge (total of 18 x 45-minute lessons over 9 weeks), data from two girls within a focus group showed that the students needed to: (1) receive clarification on engineering terms to facilitate more fluent discourse, (2) question and debate conceptual understandings without peers being judgemental, and (3) have multiple opportunities for engaging with materials towards designing, constructing and explaining key concepts learnt. Implications for teachers undertaking STEM education are evident, including outlining expectations for clarifying STEM terms, outlining to students about interacting non-judgementally, and providing multiple opportunities for interacting within engineering education.

Front interactions in a three-component system

The three-component reaction-diffusion system introduced in [C. P. Schenk et al., Phys. Rev. Lett., 78 (1997), pp. 3781–3784] has become a paradigm model in pattern formation. It exhibits a rich variety of dynamics of fronts, pulses, and spots. The front and pulse interactions range in type from weak, in which the localized structures interact only through their exponentially small tails, to strong interactions, in which they annihilate or collide and in which all components are far from equilibrium in the domains between the localized structures. Intermediate to these two extremes sits the semistrong interaction regime, in which the activator component of the front is near equilibrium in the intervals between adjacent fronts but both inhibitor components are far from equilibrium there, and hence their concentration profiles drive the front evolution. In this paper, we focus on dynamically evolving N-front solutions in the semistrong regime. The primary result is use of a renormalization group method to rigorously derive the system of N coupled ODEs that governs the positions of the fronts. The operators associated with the linearization about the N-front solutions have N small eigenvalues, and the N-front solutions may be decomposed into a component in the space spanned by the associated eigenfunctions and a component projected onto the complement of this space. This decomposition is carried out iteratively at a sequence of times. The former projections yield the ODEs for the front positions, while the latter projections are associated with remainders that we show stay small in a suitable norm during each iteration of the renormalization group method. Our results also help extend the application of the renormalization group method from the weak interaction regime for which it was initially developed to the semistrong interaction regime. The second set of results that we present is a detailed analysis of this system of ODEs, providing a classification of the possible front interactions in the cases of $N=1,2,3,4$, as well as how front solutions interact with the stationary pulse solutions studied earlier in [A. Doelman, P. van Heijster, and T. J. Kaper, J. Dynam. Differential Equations, 21 (2009), pp. 73–115; P. van Heijster, A. Doelman, and T. J. Kaper, Phys. D, 237 (2008), pp. 3335–3368]. Moreover, we present some results on the general case of N-front interactions.

Child car restraints : mandating type and seating row according to age with positive effect in regional city in Queensland, Australia

Road trauma is a leading cause of child injury worldwide. In highly motorised countries, injury as a passenger represents a major proportion of all child road deaths and hospitalisations. Australia is no exception, particularly since there are high levels of private motor vehicle travel to school in most Australian states. Recently the legislation governing the type of car restraints required for children aged under 7 years has changed in Australia, aligning requirements better with accepted best practice. However, it is unclear what effect these changes have had on children’s seating positions or the types of restraints used. A mixed methods evaluation of the impact of the new legislation on compliance was conducted at three times: baseline (Time 1); after announcement that changes were going to be implemented but before enforcement began (Time 2); and after enforcement commenced (Time 3). Measures of compliance were obtained using two methods: road-side observations of vehicles with child passengers; and parental self-report (intercept interviews conducted at Time 2 and Time 3 only). Results from the observations suggested an overall positive effect. Proportions of children occupying front seats decreased overall and use of dedicated child seats increased to almost 40% of the observed children by Time 3. However, almost a quarter of the children observed still occupied front seats. These results differed from those of the interview study where almost no children were reported as usually travelling in the front seat, and reported use of dedicated restraints with children was almost 90%, over twice that of the observations.

Suspected child abuse and neglect reporting behaviour

Executuve Summary Background and Aims Child abuse and neglect is a tragedy within our community, with over 10,000 substantiated reports of abuse and neglect in Queensland in the past year. The considerable consequences of child abuse and neglect are far-reaching, substantial and can be fatal. The reporting of suspicions of child abuse or neglect is often the first step in preventing further abuse or neglect. In the State of Queensland, medical practitioners are mandated by law to report their suspicions of child abuse and neglect. However, despite this mandate many still do not report their suspicions. A 1998 study indicated that 43% of medical practitioners had, at some time, made a conscious decision to not report suspected abuse or neglect (Van Haeringen, Dadds & Armstrong, 1998). The aim of this study was to gain a better understanding of beliefs about reporting suspected child abuse and neglect and the barriers to reporting suspected abuse and neglect by medical practitioners and parents and students. The findings have the potential to inform the training and education of members of the community who have a shared responsibility to protect the wellbeing of its most vulnerable members. Method In one of the largest studies of reporting behaviour in relation to suspected child abuse and neglect in Australia, we examined and compared medical practitioners’ responses with members of the community, namely parents and students. We surveyed 91 medical practitioners and 214 members of the community (102 parents and 112 students) regarding their beliefs and reporting behaviour related to suspected child abuse and neglect. We also examined reasons for not reporting suspected abuse or neglect, as well as awareness of responsibilities and the appropriate reporting procedures. To obtain such information, participants anonymously completed a comprehensive questionnaire using items from previous studies of reporting attitudes and behaviour. Executive Summary Abused Child Trust Report August 2003 5 Findings Key findings include: • The majority of medical practitioners (97%) were aware of their duty to report suspected abuse and neglect and believed they had a professional and ethical duty to do so. • A majority of parents (82%) and students (68%) also believed that they had a professional and ethical duty to report suspected abuse and neglect. • In accord with their statutory duty to report suspected abuse and neglect, 69% of medical practitioners had made a report at some point. • Sixteen percent of parents and 9% of students surveyed indicated that they had reported their suspicions of neglect and abuse. • The most endorsed belief associated with not reporting suspected child abuse and neglect was that, ‘unpleasant events would follow reporting’. • Over a quarter of medical practitioners (26%) admitted to making a decision not to report their suspicions of child abuse or neglect on at least one occasion. • Compared with previous research, there has been a decline in the number of medical practitioners who decided not to report suspected abuse or neglect from 43% (Van Haeringen et al., 1998) to 26% in the current study. • Fourteen percent of parents and 15% of students surveyed had also chosen not to report a case of suspected abuse or neglect. • Attitudes that most strongly influenced the decision to report or not report suspected abuse or neglect differed between groups (medical practitioners, parents, or students). A belief that, ‘the abuse was a single incident’ was the best predictor of non-reporting by medical practitioners, while having ‘no time to follow-up the report’ or failing to be ‘convinced of evidence of abuse’ best predicted failure to report abuse by students. A range of beliefs predicted non-reporting by parents, including the beliefs that reporting suspected abuse was ‘not their responsibility’ and ‘knowing the child had retracted their statement’. Conclusions Of major concern is that approximately 25% of medical practitioners with a mandated responsibility to report, as well as some members of the general public, revealed that they have suspected child neglect or abuse but have made the decision not to report their suspicions. Parents and students perceived the general community as having responsibility for reporting suspicions of abuse or neglect. Despite this perception, they felt that lodging a report may be overly demanding in terms of time and they had the confidence in their ability to identify child abuse and neglect. An explanation for medical practitioners deciding not to report may be based upon their optimistic belief that suspected abuse or neglect was a single incident. Our findings may best be understood from the ‘inflation of optimism’ hypothesis put forward by the Nobel Laureate, Daniel Kahneman. He suggests that in spite of rational evidence, human beings tend to make judgements based on an optimistic view rather than engaging in a rational decision-making process. In this case, despite past behaviour of abuse or neglect being the best predictor of future behaviour, medical practitioners have taken an optimistic view, choosing to believe that their suspicion of child abuse or neglect represents a single incident. The clear implication of findings in the current research is the need for the members of the general community and medical practitioners to be better appraised of the consequences of their decision-making in relation to suspicionsof child abuse and neglect. Finally findings from parents and students relating to their reporting behaviour suggest that members of the larger community represent an untapped resourcewho might, with appropriate awareness, play a more significant role in theidentification and reporting of suspected child abuse and neglect.

Predictive modelling : parents’ decision making to use online child health information to increase their understanding and/or diagnose or treat their child’s health

Abstract Background The quantum increases in home Internet access and available online health information with limited control over information quality highlight the necessity of exploring decision making processes in accessing and using online information, specifically in relation to children who do not make their health decisions. Objectives To understand the processes explaining parents’ decisions to use online health information for child health care. Methods Parents (N = 391) completed an initial questionnaire assessing the theory of planned behaviour constructs of attitude, subjective norm, and perceived behavioural control, as well as perceived risk, group norm, and additional demographic factors. Two months later, 187 parents completed a follow-up questionnaire assessing their decisions to use online information for their child’s health care, specifically to 1) diagnose and/or treat their child’s suspected medical condition/illness and 2) increase understanding about a diagnosis or treatment recommended by a health professional. Results Hierarchical multiple regression showed that, for both behaviours, attitude, subjective norm, perceived behavioural control, (less) perceived risk, group norm, and (non) medical background were the significant predictors of intention. For parents’ use of online child health information, for both behaviours, intention was the sole significant predictor of behaviour. The findings explain 77% of the variance in parents’ intention to treat/diagnose a child health problem and 74% of the variance in their intentions to increase their understanding about child health concerns. Conclusions Understanding parents’ socio-cognitive processes that guide their use of online information for child health care is important given the increase in Internet usage and the sometimes-questionable quality of health information provided online. Findings highlight parents’ thirst for information; there is an urgent need for health professionals to provide parents with evidence-based child health websites in addition to general population education on how to evaluate the quality of online health information.

Eat Cook Grow : Mixing Human-Computer Interactions with Human-Food Interactions

Food has been a major agenda in political, socio-cultural, and environmental domains throughout history. The significance of food has been particularly highlighted in recent years with the growing public awareness of the unfolding impacts of climate change, challenging our understanding, practice, and expectations of our relationship with food. Parallel to this development has been the rise of web applications such as blogs, wikis, video and photo sharing sites, and social networking systems that are arguably more open, collaborative, and personalisable. These so-called ‘Web 2.0’ technologies have contributed to a more participatory Internet experience than what had previously been possible. An increasing number of these social applications are now available on mobile technologies where they take advantage of device-specific features such as sensors, location and context awareness, further expanding potential for the culture of participation and creativity. This international volume assembles a diverse collection of book chapters that contribute towards exploring and better understanding the opportunities and challenges provided by tools, interfaces, methods, and practices of social and mobile technology to enable engagement with people and creativity in the domain of food in contemporary society. It brings together an international group of academics and practitioners from a diverse range of disciplines such as computing and engineering, social sciences, digital media and human-computer interaction to critically examine a range of applications of social and mobile technology, such as social networking, mobile interaction, wikis, twitter, blogging, mapping, shared displays and urban screens, and their impact to foster a better understanding and practice of environmentally, socio-culturally, economically, and health-wise sustainable food culture.

Imaging fluid solid interactions in hydrocarbon reservoir rocks

The environmental scanning electron microscope (ESEM) has been used to image liquid hydrocarbons in sandstones and oil shales. Additionally, the fluid sensitivity of selected clay minerals in hydrocarbon reservoirs was assessed via three case studies: HCl acid sensitivity of authigenic chlorite in sandstone reservoirs, freshwater sensitivity of authigenic illite/smectite in sandstone reservoirs, and bleach sensitivity of a volcanic reservoir containing abundant secondary chlorite/corrensite. The results showed the suitability of using ESEM for imaging liquid hydrocarbon films in hydrocarbon reservoirs and the importance of simulating in situ fluid-rock interactions for hydrocarbon production programmes. In each case, results of the ESEM studies greatly enhanced prediction of reservoir/borehole reactions and, in some cases, contradicted conventional wisdom regarding the outcome of potential engineering solutions. (C) 1993 Wiley-Liss, Inc.

Child rearing Inc : On the perils of political paralysis Down Under

In his 2007 PESA keynote address, Paul Smeyers discussed the increasing regulation of child-rearing through government intervention and the generation of “experts,” citing particular examples from Europe where cases of childhood obesity and parental neglect have stirred public opinion and political debate. In his paper (this issue), Smeyers touches on a number of tensions before concluding that child rearing qualifies as a practice in which liberal governments should be reluctant to intervene. In response, I draw on recent experiences in Australia and argue that certain tragic events of late are the result of an ethical, moral and social vacuum in which these tensions coalesce. While I agree with Smeyers that governments should be reluctant to “intervene” in the private domain of the family, I argue that there is a difference between intervention and support. In concluding, I maintain that if certain Western liberal democracies did a more comprehensive job of supporting children and their families through active social investment in primary school education, then both families and schools would be better equipped to deal with the challenges they now face.

In defence of Victoria's Children's Court : its value and role in the child protection system

Australian child protection systems have been subject to sustained and significant criticism for many decades. As a central part of that system Children’s Courts have been implicated: three recent inquiries into the child protection system in Victoria all criticised the Family Division of the Children’s Court.1 In the resulting debate two diametrically opposed points of view surfaced about the Children’s Court and the role that legal procedures and professionals should play in child protection matters. On one side bodies like the Children’s Court of Victoria, Victoria Legal Aid (‘VLA’), the Law Institute of Victoria (‘LIV’), and the Federation of Community Legal Centres (‘FCLC’) argued that the Children’s Court plays a vital role in child protection and should continue to play that role.2 On the other side a coalition of human service and child protection agencies called for major change including the removal of the Children’s Court from the child protection system. Victoria’s Department of Human Services (‘DHS’) has been critical of the Court3 as have community sector organisations like Anglicare, Berry Street, MacKillop Family Services and the Salvation Army — all agencies the DHS funds to deliver child protection services.4 Victoria’s Child Safety Commissioner has also called for major reform, publicly labelling the Court a ‘lawyers’ playground’ and recommending abolishing the Court’s involvement in child protection completely.

The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions

Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of COPII and clathrin coats assembled in vitro without membranes suggest that coat components assemble regular cages with the same set of interactions between components. Detailed three-dimensional structures of coated membrane vesicles have not been obtained. Here, we solved the structures of individual COPI-coated membrane vesicles by cryoelectron tomography and subtomogram averaging of in vitro reconstituted budding reactions. The coat protein complex, coatomer, was observed to adopt alternative conformations to change the number of other coatomers with which it interacts and to form vesicles with variable sizes and shapes. This represents a fundamentally different basis for vesicle coat assembly.