Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Negotiating social and moral order in internet relay chat

Although internet chat is a significant aspect of many internet users’ lives, the manner in which participants in quasi-synchronous chat situations orient to issues of social and moral order remains to be studied in depth. The research presented here is therefore at the forefront of a continually developing area of study. This work contributes new insights into how members construct and make accountable the social and moral orders of an adult-oriented Internet Relay Chat (IRC) channel by addressing three questions: (1) What conversational resources do participants use in addressing matters of social and moral order? (2) How are these conversational resources deployed within IRC interaction? and (3) What interactional work is locally accomplished through use of these resources? A survey of the literature reveals considerable research in the field of computer-mediated communication, exploring both asynchronous and quasi-synchronous discussion forums. The research discussed represents a range of communication interests including group and collaborative interaction, the linguistic construction of social identity, and the linguistic features of online interaction. It is suggested that the present research differs from previous studies in three ways: (1) it focuses on the interaction itself, rather than the ways in which the medium affects the interaction; (2) it offers turn-by-turn analysis of interaction in situ; and (3) it discusses membership categories only insofar as they are shown to be relevant by participants through their talk. Through consideration of the literature, the present study is firmly situated within the broader computer-mediated communication field. Ethnomethodology, conversation analysis and membership categorization analysis were adopted as appropriate methodological approaches to explore the research focus on interaction in situ, and in particular to investigate the ways in which participants negotiate and co-construct social and moral orders in the course of their interaction. IRC logs collected from one chat room were analysed using a two-pass method, based on a modification of the approaches proposed by Pomerantz and Fehr (1997) and ten Have (1999). From this detailed examination of the data corpus three interaction topics are identified by means of which participants clearly orient to issues of social and moral order: challenges to rule violations, ‘trolling’ for cybersex, and experiences regarding the 9/11 attacks. Instances of these interactional topics are subjected to fine-grained analysis, to demonstrate the ways in which participants draw upon various interactional resources in their negotiation and construction of channel social and moral orders. While these analytical topics stand alone in individual focus, together they illustrate different instances in which participants’ talk serves to negotiate social and moral orders or collaboratively construct new orders. Building on the work of Vallis (2001), Chapter 5 illustrates three ways that rule violation is initiated as a channel discussion topic: (1) through a visible violation in open channel, (2) through an official warning or sanction by a channel operator regarding the violation, and (3) through a complaint or announcement of a rule violation by a non-channel operator participant. Once the topic has been initiated, it is shown to become available as a topic for others, including the perceived violator. The fine-grained analysis of challenges to rule violations ultimately demonstrates that channel participants orient to the rules as a resource in developing categorizations of both the rule violation and violator. These categorizations are contextual in that they are locally based and understood within specific contexts and practices. Thus, it is shown that compliance with rules and an orientation to rule violations as inappropriate within the social and moral orders of the channel serves two purposes: (1) to orient the speaker as a group member, and (2) to reinforce the social and moral orders of the group. Chapter 6 explores a particular type of rule violation, solicitations for ‘cybersex’ known in IRC parlance as ‘trolling’. In responding to trolling violations participants are demonstrated to use affiliative and aggressive humour, in particular irony, sarcasm and insults. These conversational resources perform solidarity building within the group, positioning non-Troll respondents as compliant group members. This solidarity work is shown to have three outcomes: (1) consensus building, (2) collaborative construction of group membership, and (3) the continued construction and negotiation of existing social and moral orders. Chapter 7, the final data analysis chapter, offers insight into how participants, in discussing the events of 9/11 on the actual day, collaboratively constructed new social and moral orders, while orienting to issues of appropriate and reasonable emotional responses. This analysis demonstrates how participants go about ‘doing being ordinary’ (Sacks, 1992b) in formulating their ‘first thoughts’ (Jefferson, 2004). Through sharing their initial impressions of the event, participants perform support work within the interaction, in essence working to normalize both the event and their initial misinterpretation of it. Normalising as a support work mechanism is also shown in relation to participants constructing the ‘quiet’ following the event as unusual. Normalising is accomplished by reference to the indexical ‘it’ and location formulations, which participants use both to negotiate who can claim to experience the ‘unnatural quiet’ and to identify the extent of the quiet. Through their talk participants upgrade the quiet from something legitimately experienced by one person in a particular place to something that could be experienced ‘anywhere’, moving the phenomenon from local to global provenance. With its methodological design and detailed analysis and findings, this research contributes to existing knowledge in four ways. First, it shows how rules are used by participants as a resource in negotiating and constructing social and moral orders. Second, it demonstrates that irony, sarcasm and insults are three devices of humour which can be used to perform solidarity work and reinforce existing social and moral orders. Third, it demonstrates how new social and moral orders are collaboratively constructed in relation to extraordinary events, which serve to frame the event and evoke reasonable responses for participants. And last, the detailed analysis and findings further support the use of conversation analysis and membership categorization as valuable methods for approaching quasi-synchronous computer-mediated communication.

Building procurement methods

A plethora of methods for procuring building projects are available to meet the needs of clients. Deciding what method to use for a given project is a difficult and challenging task as a client’s objectives and priorities need to marry with the selected method so as to improve the likelihood of the project being procured successfully. The decision as to what procurement system to use should be made as early as possible and underpinned by the client’s business case for the project. The risks and how they can potentially affect the client’s business should also be considered. In this report, the need for client’s to develop a procurement strategy, which outlines the key means by which the objectives of the project are to be achieved is emphasised. Once a client has established a business case for a project, appointed a principal advisor, determined their requirements and brief, then consideration as to which procurement method to be adopted should be made. An understanding of the characteristics of various procurement options is required before a recommendation can be made to a client. Procurement systems can be categorised as traditional, design and construct, management and collaborative. The characteristics of these systems along with the procurement methods commonly used are described. The main advantages and disadvantages, and circumstances under which a system could be considered applicable for a given project are also identified.

Investment decision-making under risk (reliability) and uncertainty for infrastructure asset management

Risks and uncertainties are inevitable in engineering projects and infrastructure investments. Decisions about investment in infrastructure such as for maintenance, rehabilitation and construction works can pose risks, and may generate significant impacts on social, cultural, environmental and other related issues. This report presents the results of a literature review of current practice in identifying, quantifying and managing risks and predicting impacts as part of the planning and assessment process for infrastructure investment proposals. In assessing proposals for investment in infrastructure, it is necessary to consider social, cultural and environmental risks and impacts to the overall community, as well as financial risks to the investor. The report defines and explains the concept of risk and uncertainty, and describes the three main methodology approaches to the analysis of risk and uncertainty in investment planning for infrastructure, viz examining a range of scenarios or options, sensitivity analysis, and a statistical probability approach, listed here in order of increasing merit and complexity. Forecasts of costs, benefits and community impacts of infrastructure are recognised as central aspects of developing and assessing investment proposals. Increasingly complex modelling techniques are being used for investment evaluation. The literature review identified forecasting errors as the major cause of risk. The report contains a summary of the broad nature of decision-making tools used by governments and other organisations in Australia, New Zealand, Europe and North America, and shows their overall approach to risk assessment in assessing public infrastructure proposals. While there are established techniques to quantify financial and economic risks, quantification is far less developed for political, social and environmental risks and impacts. The report contains a summary of the broad nature of decision-making tools used by governments and other organisations in Australia, New Zealand, Europe and North America, and shows their overall approach to risk assessment in assessing public infrastructure proposals. While there are established techniques to quantify financial and economic risks, quantification is far less developed for political, social and environmental risks and impacts. For risks that cannot be readily quantified, assessment techniques commonly include classification or rating systems for likelihood and consequence. The report outlines the system used by the Australian Defence Organisation and in the Australian Standard on risk management. After each risk is identified and quantified or rated, consideration can be given to reducing the risk, and managing any remaining risk as part of the scope of the project. The literature review identified use of risk mapping techniques by a North American chemical company and by the Australian Defence Organisation. This literature review has enabled a risk assessment strategy to be developed, and will underpin an examination of the feasibility of developing a risk assessment capability using a probability approach.

Passive control of a bi-ventricular assist device : an experimental and numerical investigation

For the last two decades heart disease has been the highest single cause of death for the human population. With an alarming number of patients requiring heart transplant, and donations not able to satisfy the demand, treatment looks to mechanical alternatives. Rotary Ventricular Assist Devices, VADs, are miniature pumps which can be implanted alongside the heart to assist its pumping function. These constant flow devices are smaller, more efficient and promise a longer operational life than more traditional pulsatile VADs. The development of rotary VADs has focused on single pumps assisting the left ventricle only to supply blood for the body. In many patients however, failure of both ventricles demands that an additional pulsatile device be used to support the failing right ventricle. This condition renders them hospital bound while they wait for an unlikely heart donation. Reported attempts to use two rotary pumps to support both ventricles concurrently have warned of inherent haemodynamic instability. Poor balancing of the pumps’ flow rates quickly leads to vascular congestion increasing the risk of oedema and ventricular ‘suckdown’ occluding the inlet to the pump. This thesis introduces a novel Bi-Ventricular Assist Device (BiVAD) configuration where the pump outputs are passively balanced by vascular pressure. The BiVAD consists of two rotary pumps straddling the mechanical passive controller. Fluctuations in vascular pressure induce small deflections within both pumps adjusting their outputs allowing them to maintain arterial pressure. To optimise the passive controller’s interaction with the circulation, the controller’s dynamic response is optimised with a spring, mass, damper arrangement. This two part study presents a comprehensive assessment of the prototype’s ‘viability’ as a support device. Its ‘viability’ was considered based on its sensitivity to pathogenic haemodynamics and the ability of the passive response to maintain healthy circulation. The first part of the study is an experimental investigation where a prototype device was designed and built, and then tested in a pulsatile mock circulation loop. The BiVAD was subjected to a range of haemodynamic imbalances as well as a dynamic analysis to assess the functionality of the mechanical damper. The second part introduces the development of a numerical program to simulate human circulation supported by the passively controlled BiVAD. Both investigations showed that the prototype was able to mimic the native baroreceptor response. Simulating hypertension, poor flow balancing and subsequent ventricular failure during BiVAD support allowed the passive controller’s response to be assessed. Triggered by the resulting pressure imbalance, the controller responded by passively adjusting the VAD outputs in order to maintain healthy arterial pressures. This baroreceptor-like response demonstrated the inherent stability of the auto regulating BiVAD prototype. Simulating pulmonary hypertension in the more observable numerical model, however, revealed a serious issue with the passive response. The subsequent decrease in venous return into the left heart went unnoticed by the passive controller. Meanwhile the coupled nature of the passive response not only decreased RVAD output to reduce pulmonary arterial pressure, but it also increased LVAD output. Consequently, the LVAD increased fluid evacuation from the left ventricle, LV, and so actually accelerated the onset of LV collapse. It was concluded that despite the inherently stable baroreceptor-like response of the passive controller, its lack of sensitivity to venous return made it unviable in its present configuration. The study revealed a number of other important findings. Perhaps the most significant was that the reduced pulse experienced during constant flow support unbalanced the ratio of effective resistances of both vascular circuits. Even during steady rotary support therefore, the resulting ventricle volume imbalance increased the likelihood of suckdown. Additionally, mechanical damping of the passive controller’s response successfully filtered out pressure fluctuations from residual ventricular function. Finally, the importance of recognising inertial contributions to blood flow in the atria and ventricles in a numerical simulation were highlighted. This thesis documents the first attempt to create a fully auto regulated rotary cardiac assist device. Initial results encourage development of an inlet configuration sensitive to low flow such as collapsible inlet cannulae. Combining this with the existing baroreceptor-like response of the passive controller will render a highly stable passively controlled BiVAD configuration. The prototype controller’s passive interaction with the vasculature is a significant step towards a highly stable new generation of artificial heart.

Enhancing research and development: designing collaborative environments for innovation

Work environments have previously been studied to identify the strategies, structures and processes which increase the likelihood of creativity, innovation and collaboration for productive workplaces. A number of perspectives have emerged which identify social and cognitive factors known to contribute to or to restrict innovation and collaboration. Recently more attention has been given to designing physical environments to encourage processes relevant to innovation such as creativity (McCoy & Evans, 2002) knowledge sharing (Hemlin, Allwood & Martin, 2008) and collaboration (Bozeman & Corley, 2004). Some attention has been given specifically to research and development environments (Boutellier et al, 2008) but little integration of this research has occurred. In the context of the construction of new purpose-built premises which will bring together under one roof separate public sector agencies engaged in research and development in agriculture, natural resource systems and the environment, this paper examines the extant literature and develops initial propositions for research relevant to the transition, collaboration and performance of research and development in new organizational environments where traditional boundaries have been redrawn.

Managing knowledge in an outsourcing environment

What an organisation does versus what it out-sources to the market is a classic boundaries of the firm question that has previously been dominated by efficiency arguments. However, a knowledge-based view suggests these boundaries are integral to the ability of a firm to deploy existing knowledge stocks efficiently, as well as develop new knowledge through learning that will drive future competitiveness. Furthermore, the nature of these boundaries, in respect of their permeability is critical in understanding the likelihood of knowledge flowing into and out of the organisation. Using these concepts, we present a case study of Main Roads Western Australia to illustrate how these principles have allowed it to start rebuilding its internal capabilities through repositioning its operational boundaries and via ensuring their boundaries are highly porous as they move more major projects into alliance contracts.

Sustainable construction for the future - the role of government in energy efficiency and sustainability in buildings

This paper will summarise the findings from a study that explored the link between dwelling design, or type, and energy efficiencies in sub-tropical climates. An increasing number of government and private sector development companies are initiating projects that aim to deliver enhanced environmental outcomes at both sub-divisional and dwelling levels. The study used AccuRate, a new thermal modelling tool developed by CSIRO that responds to the need to improve ventilation modelling. The study found that dwellings developed in conjunction with the Departments of Housing and Public Works have set the benchmark. It provides a snapshot of the energy efficiency of a range of dwelling types found in recent subdivisions. However, the trend toward increasing urban densities may reduce the likelihood that cooling breezes will be available to cool dwellings. The findings are relevant to regulators, designers and industry in all states interested in reducing the energy used to cool dwellings in summer.

Best Practice Guide : Clients

The Guide contains the distilled findings from a major, two-year research project to explore those factors considered by industry practitioners to be critical to the successful adoption of ICT, both within their firms and between their firms and their trading partners. In the context of this project Critical Success Factors (CSFs) have been defined as, “Those things that absolutely, positively must be attended to in order to maximise the likelihood of a successful outcome for the stakeholder, defined in the stakeholder’s terms.” The guide includes: o Perceived benefits of ICT use across the head contractors’ sector o Types and levels of ICT used across the sector o Self-assessment tool o CSFs for high-level ICT users, including o Best Practice Profiles o Action Statements The material contained in this Guide has been generated following a number of principles: o For a given situation there is not a single ‘right answer’, but a number of solutions that have to be evaluated using a range of relevant factors. o Since there are as many solutions as there are ‘solvers’, factors for evaluation will ‘emerge’ from collective wisdom.

Best Practice Guide : Consultants

The Guide contains the distilled findings from a major, two-year research project to explore those factors considered by industry practitioners to be critical to the successful adoption of ICT, both within their firms and between their firms and their trading partners. In the context of this project Critical Success Factors (CSFs) have been defined as, “Those things that absolutely, positively must be attended to in order to maximise the likelihood of a successful outcome for the stakeholder, defined in the stakeholder’s terms.” The guide includes: o Perceived benefits of ICT use across the consultants’ sector o Types and levels of ICT used across the sector o Self-assessment tool o CSFs for medium- and high-level ICT users, including o Best Practice Profiles o Action Statements o Barriers to ICT use for low-level users o Action Statements The material contained in this Guide has been generated following a number of principles: o For a given situation there is not a single ‘right answer’, but a number of solutions that have to be evaluated using a range of relevant factors. o As there are as many solutions as there are ‘solvers’, factors for evaluation will ‘emerge’ from collective wisdom.

Best Practice Guide : Head Contractors

The Guide contains the distilled findings from a major, two-year research project to explore those factors considered by industry practitioners to be critical to the successful adoption of ICT, both within their firms and between their firms and their trading partners. In the context of this project Critical Success Factors (CSFs) have been defined as, “Those things that absolutely, positively must be attended to in order to maximise the likelihood of a successful outcome for the stakeholder, defined in the stakeholder’s terms.” The guide includes: o Perceived benefits of ICT use across the head contractors’ sector o Types and levels of ICT used across the sector o Self-assessment tool o CSFs for medium- and high-level ICT users, including o Best Practice Profiles o Action Statements The material contained in this Guide has been generated following a number of principles: o For a given situation there is not a single ‘right answer’, but a number of solutions that have to be evaluated using a range of relevant factors. o Since there are as many solutions as there are ‘solvers’, factors for evaluation will ‘emerge’ from collective wisdom.

Best Practice Guide : Subcontractors

The Guide contains the distilled findings from a major, two-year research project to explore those factors considered by industry practitioners to be critical to the successful adoption of ICT, both within their firms and between their firms and their trading partners. In the context of this project Critical Success Factors (CSFs) have been defined as, “Those things that absolutely, positively must be attended to in order to maximise the likelihood of a successful outcome for the stakeholder, defined in the stakeholder’s terms.” The guide includes: o Perceived benefits of ICT use across the subcontractors’ sector o Types and levels of ICT used across the sector o Self-assessment tool o CSFs for medium- and high-level ICT users, including o Best Practice Profiles o Action Statements o Barriers to ICT use for low-level users o Action Statements The material contained in this Guide has been generated following a number of principles: o For a given situation there is not a single ‘right answer’, but a number of solutions that have to be evaluated using a range of relevant factors. o As there are as many solutions as there are ‘solvers’, factors for evaluation will ‘emerge’ from collective wisdom.

Discourse practice gaps in work life balance : comparative case studies in the Australian construction industry

Perspectives on work-life balance (WLB) reflected in political, media and organisational discourse, would maintain that WLB is on the agenda because of broad social, economic and political factors (Fleetwood 2007). In contrast, critical scholarship which examines work-life balance (WLB) and its associated practices maintains that workplace flexibility is more than a quasi-functionalist response to contemporary problems faced by individuals, families or organisations. For example, the literature identifies where flexible work arrangements have not lived up to expectations of a panacea for work-home conflicts, being characterised as much by employer-driven working conditions that disadvantage workers and constrain balance, as they are by employee friendly practices that enable it (Charlesworth 1997). Further, even where generous organisational work-life balance policies exist, under-utilisation is an issue (Schaefer et al, 2007). Compounding these issues is that many employees perceive their paid work as becoming more intense, pressured and demanding (Townsend et al 2003).

Continuation rates and reasons for removal among Implanon® users accessing two family planning clinics in Queensland, Australia

Background - This study examined demographic profile, continuation rates and reasons for removal among Implanon^® users accessing two family planning clinics in Queensland, Australia. Study Design - A retrospective chart audit of 976 women who attended for implant insertion over a 3-year period between May 2001 and May 2004. Results - Continuation rates showed that at 6 months after insertion, 94% of women continued, 74% continued at 1 year and 50% continued at 2 years. Metropolitan women were more likely than rural women to discontinue use because of dissatisfaction with bleeding patterns. Cox regression analysis showed that those attending the regional clinic experienced significantly shorter time to removal. Conclusions - Implanon® continuation rates and reasons for removal differ between clinics in metropolitan and rural locations. A cooling-off period did not affect the likelihood of continuation with Implanon®. Preinsertion counselling should emphasize potential changes in bleeding patterns.

Intentions and willingness to use complementary and alternative medicines : what potential patients believe about CAMs

This paper explores the intentions and willingness of a sample of Australian consumers (N = 356) to use Complementary and Alternative Medicine (CAM). Participants considered using CAMs at least once in the next two months and rated the likelihood of certain consequences of CAM use, whether important others would approve, and if barriers would prevent them from using CAMs. People intending to use CAMs (high intenders) were more likely than those low on intention (low intenders) to endorse positive outcomes of CAM use and believe that important others would support their CAM use. High intenders were less likely than low intenders to believe that barriers would prevent use. Low intenders (n = 200) were also asked to consider their response to a free CAM trial. Those willing to accept a trial were more likely than those unwilling to believe that CAMs could improve health and less likely to believe that laziness would prevent use. These results identify important beliefs which may influence people’s decisions to use CAMs.