Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Evidence for time dependency of molecular rate estimates

Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

Use of Bayesian MUNE to show differing rate of loss of motor units in subgroups of ALS

Objectives To evaluate differences among patients with different clinical features of ALS, we used our Bayesian method of motor unit number estimation (MUNE). Methods We performed serial MUNE studies on 42 subjects who fulfilled the diagnostic criteria for ALS during the course of their illness. Subjects were classified into three subgroups according to whether they had typical ALS (with upper and lower motor neurone signs) or had predominantly upper motor neurone weakness with only minor LMN signs, or predominantly lower motor neurone weakness with only minor UMN signs. In all subjects we calculated the half life of MUs, defined as the expected time for the number of MUs to halve, in one or more of the abductor digiti minimi (ADM), abductor pollicis brevis (APB) and extensor digitorum brevis (EDB) muscles. Results The mean half life of MUs was less in subjects who had typical ALS with both upper and lower motor neurone signs than in those with predominantly upper motor neurone weakness or predominantly lower motor neurone weakness. In 18 subjects we analysed the estimated size of the MUs and demonstrated the appearance of large MUs in subjects with upper or lower motor neurone predominant weakness. We found that the appearance of large MUs was correlated with the half life of MUs. Conclusions Patients with different clinical features of ALS have different rates of loss and different sizes of MUs. Significance: These findings could indicate differences in disease pathogenesis.

Enhancing student success and retention : an institution-wide strategy for peer programs

Higher Education's widening participation agenda prioritises improving access to university for low-SES students. Parallel with these ambitious national participation targets, is the challenge for universities to significantly improve student retention rates; hence, the need to implement strategies aimed to improve the quality of the student learning experience and build a 'sense of belonging'. Within the framework of the First Year Experience Program, Queensland University of Technology has embarked on establishing a whole-of-institution model for peer programs that aims to: 1) improve the student learning experience and outcomes; and, 2) establish quality assured and sustainable programs. This paper reports on the maturation university-wide peer program strategy and considers the challenges of implementing, evaluating and resourcing a sustainable and inclusive approach to peer programs.

A transition pedagogy for student engagement and first-year learning, success and retention

This chapter argues that higher education institutions (HEIs) must direct coordinated, whole-of-institution attention to changing, both culturally and structurally, the fundamental and prevailing character of the first-year experience (FYE). It leverages evidence from the sector(Nelson, Kift and Clarke, 2011), from research-led practice in our institution (for example, Kift, Nelson and Clarke, 2010; Nelson et al.,in press) and from research conducted under an Australian Learning and Teaching Council Senior Fellowship (Kift, 2009a, 2009b, 2009c) to assert that student engagement and success should not be left to chance, particularly those aspects such as curriculum design and enactment that are within our institutional control.

Experimental studies of wireless communication and GNSS kinematic positioning performance in high-mobility vehicle environments

In order to support intelligent transportation system (ITS) road safety applications such as collision avoidance, lane departure warnings and lane keeping, Global Navigation Satellite Systems (GNSS) based vehicle positioning system has to provide lane-level (0.5 to 1 m) or even in-lane-level (0.1 to 0.3 m) accurate and reliable positioning information to vehicle users. However, current vehicle navigation systems equipped with a single frequency GPS receiver can only provide road-level accuracy at 5-10 meters. The positioning accuracy can be improved to sub-meter or higher with the augmented GNSS techniques such as Real Time Kinematic (RTK) and Precise Point Positioning (PPP) which have been traditionally used in land surveying and or in slowly moving environment. In these techniques, GNSS corrections data generated from a local or regional or global network of GNSS ground stations are broadcast to the users via various communication data links, mostly 3G cellular networks and communication satellites. This research aimed to investigate the precise positioning system performances when operating in the high mobility environments. This involves evaluation of the performances of both RTK and PPP techniques using: i) the state-of-art dual frequency GPS receiver; and ii) low-cost single frequency GNSS receiver. Additionally, this research evaluates the effectiveness of several operational strategies in reducing the load on data communication networks due to correction data transmission, which may be problematic for the future wide-area ITS services deployment. These strategies include the use of different data transmission protocols, different correction data format standards, and correction data transmission at the less-frequent interval. A series of field experiments were designed and conducted for each research task. Firstly, the performances of RTK and PPP techniques were evaluated in both static and kinematic (highway with speed exceed 80km) experiments. RTK solutions achieved the RMS precision of 0.09 to 0.2 meter accuracy in static and 0.2 to 0.3 meter in kinematic tests, while PPP reported 0.5 to 1.5 meters in static and 1 to 1.8 meter in kinematic tests by using the RTKlib software. These RMS precision values could be further improved if the better RTK and PPP algorithms are adopted. The tests results also showed that RTK may be more suitable in the lane-level accuracy vehicle positioning. The professional grade (dual frequency) and mass-market grade (single frequency) GNSS receivers were tested for their performance using RTK in static and kinematic modes. The analysis has shown that mass-market grade receivers provide the good solution continuity, although the overall positioning accuracy is worse than the professional grade receivers. In an attempt to reduce the load on data communication network, we firstly evaluate the use of different correction data format standards, namely RTCM version 2.x and RTCM version 3.0 format. A 24 hours transmission test was conducted to compare the network throughput. The results have shown that 66% of network throughput reduction can be achieved by using the newer RTCM version 3.0, comparing to the older RTCM version 2.x format. Secondly, experiments were conducted to examine the use of two data transmission protocols, TCP and UDP, for correction data transmission through the Telstra 3G cellular network. The performance of each transmission method was analysed in terms of packet transmission latency, packet dropout, packet throughput, packet retransmission rate etc. The overall network throughput and latency of UDP data transmission are 76.5% and 83.6% of TCP data transmission, while the overall accuracy of positioning solutions remains in the same level. Additionally, due to the nature of UDP transmission, it is also found that 0.17% of UDP packets were lost during the kinematic tests, but this loss doesn't lead to significant reduction of the quality of positioning results. The experimental results from the static and the kinematic field tests have also shown that the mobile network communication may be blocked for a couple of seconds, but the positioning solutions can be kept at the required accuracy level by setting of the Age of Differential. Finally, we investigate the effects of using less-frequent correction data (transmitted at 1, 5, 10, 15, 20, 30 and 60 seconds interval) on the precise positioning system. As the time interval increasing, the percentage of ambiguity fixed solutions gradually decreases, while the positioning error increases from 0.1 to 0.5 meter. The results showed the position accuracy could still be kept at the in-lane-level (0.1 to 0.3 m) when using up to 20 seconds interval correction data transmission.

An analysis of holding cost impact on housing affordability in relation to midsized Greenfield residential property developments in South East Queensland

The position of housing demand and supply is not consistent. The Australian situation counters the experience demonstrated in many other parts of the world in the aftermath of the Global Financial Crisis, with residential housing prices proving particularly resilient. A seemingly inexorable housing demand remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of population growth fuelled by immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand level ensures problems related to housing affordability continue almost unabated. A significant, but less visible factor impacting housing affordability relates to holding costs. Although only one contributor in the housing affordability matrix, the nature and extent of holding cost impact requires elucidation: for example, the computation and methodology behind the calculation of holding costs varies widely - and in some instances completely ignored. In addition, ambiguity exists in terms of the inclusion of various elements that comprise holding costs, thereby affecting the assessment of their relative contribution. Such anomalies may be explained by considering that assessment is conducted over time in an ever-changing environment. A strong relationship with opportunity cost - in turn dependant inter alia upon prevailing inflation and / or interest rates - adds further complexity. By extending research in the general area of housing affordability, this thesis seeks to provide a detailed investigation of those elements related to holding costs specifically in the context of midsized (i.e. between 15-200 lots) greenfield residential property developments in South East Queensland. With the dimensions of holding costs and their influence over housing affordability determined, the null hypothesis H0 that holding costs are not passed on can be addressed. Arriving at these conclusions involves the development of robust economic and econometric models which seek to clarify the componentry impacts of holding cost elements. An explanatory sequential design research methodology has been adopted, whereby the compilation and analysis of quantitative data and the development of an economic model is informed by the subsequent collection and analysis of primarily qualitative data derived from surveying development related organisations. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

The maturity model concept as framework for assessing the capability of higher education institutions to address student engagement, success and retention : new horizon or false dawn?

While the engagement, success and retention of first year students are ongoing issues in higher education, they are currently of considerable and increasing importance as the pressures on teaching and learning from the new standards framework and performance funding intensifies. This Nuts & Bolts presentation introduces the concept of a maturity model and its application to the assessment of the capability of higher education institutions to address student engagement, success and retention. Participants will be provided with (a) a concise description of the concept and features of a maturity model; and (b) the opportunity to explore the potential application of maturity models (i) to the management of student engagement and retention programs and strategies within an institution and (ii) to the improvement of these features by benchmarking across the sector.

Relative entropy rate based model selection for linear hybrid system filters of uncertain nonlinear systems

Hybrid system representations have been exploited in a number of challenging modelling situations, including situations where the original nonlinear dynamics are too complex (or too imprecisely known) to be directly filtered. Unfortunately, the question of how to best design suitable hybrid system models has not yet been fully addressed, particularly in the situations involving model uncertainty. This paper proposes a novel joint state-measurement relative entropy rate based approach for design of hybrid system filters in the presence of (parameterised) model uncertainty. We also present a design approach suitable for suboptimal hybrid system filters. The benefits of our proposed approaches are illustrated through design examples and simulation studies.

Evaluating the success of large-scale, integrated information systems through the lens of IS-impact and IS-support

This study proceeds from a central interest in the importance of systematically evaluating operational large-scale integrated information systems (IS) in organisations. The study is conducted within the IS-Impact Research Track at Queensland University of Technology (QUT). The goal of the IS-Impact Track is, "to develop the most widely employed model for benchmarking information systems in organizations for the joint benefit of both research and practice" (Gable et al, 2009). The track espouses programmatic research having the principles of incrementalism, tenacity, holism and generalisability through replication and extension research strategies. Track efforts have yielded the bicameral IS-Impact measurement model; the ‘impact’ half includes Organisational-Impact and Individual-Impact dimensions; the ‘quality’ half includes System-Quality and Information-Quality dimensions. Akin to Gregor’s (2006) analytic theory, the ISImpact model is conceptualised as a formative, multidimensional index and is defined as "a measure at a point in time, of the stream of net benefits from the IS, to date and anticipated, as perceived by all key-user-groups" (Gable et al., 2008, p: 381). The study adopts the IS-Impact model (Gable, et al., 2008) as its core theory base. Prior work within the IS-Impact track has been consciously constrained to Financial IS for their homogeneity. This study adopts a context-extension strategy (Berthon et al., 2002) with the aim "to further validate and extend the IS-Impact measurement model in a new context - i.e. a different IS - Human Resources (HR)". The overarching research question is: "How can the impacts of large-scale integrated HR applications be effectively and efficiently benchmarked?" This managerial question (Cooper & Emory, 1995) decomposes into two more specific research questions – In the new HR context: (RQ1): "Is the IS-Impact model complete?" (RQ2): "Is the ISImpact model valid as a 1st-order formative, 2nd-order formative multidimensional construct?" The study adhered to the two-phase approach of Gable et al. (2008) to hypothesise and validate a measurement model. The initial ‘exploratory phase’ employed a zero base qualitative approach to re-instantiating the IS-Impact model in the HR context. The subsequent ‘confirmatory phase’ sought to validate the resultant hypothesised measurement model against newly gathered quantitative data. The unit of analysis for the study is the application, ‘ALESCO’, an integrated large-scale HR application implemented at Queensland University of Technology (QUT), a large Australian university (with approximately 40,000 students and 5000 staff). Target respondents of both study phases were ALESCO key-user-groups: strategic users, management users, operational users and technical users, who directly use ALESCO or its outputs. An open-ended, qualitative survey was employed in the exploratory phase, with the objective of exploring the completeness and applicability of the IS-Impact model’s dimensions and measures in the new context, and to conceptualise any resultant model changes to be operationalised in the confirmatory phase. Responses from 134 ALESCO users to the main survey question, "What do you consider have been the impacts of the ALESCO (HR) system in your division/department since its implementation?" were decomposed into 425 ‘impact citations.’ Citation mapping using a deductive (top-down) content analysis approach instantiated all dimensions and measures of the IS-Impact model, evidencing its content validity in the new context. Seeking to probe additional (perhaps negative) impacts; the survey included the additional open question "In your opinion, what can be done better to improve the ALESCO (HR) system?" Responses to this question decomposed into a further 107 citations which in the main did not map to IS-Impact, but rather coalesced around the concept of IS-Support. Deductively drawing from relevant literature, and working inductively from the unmapped citations, the new ‘IS-Support’ construct, including the four formative dimensions (i) training, (ii) documentation, (iii) assistance, and (iv) authorisation (each having reflective measures), was defined as: "a measure at a point in time, of the support, the [HR] information system key-user groups receive to increase their capabilities in utilising the system." Thus, a further goal of the study became validation of the IS-Support construct, suggesting the research question (RQ3): "Is IS-Support valid as a 1st-order reflective, 2nd-order formative multidimensional construct?" With the aim of validating IS-Impact within its nomological net (identification through structural relations), as in prior work, Satisfaction was hypothesised as its immediate consequence. The IS-Support construct having derived from a question intended to probe IS-Impacts, too was hypothesised as antecedent to Satisfaction, thereby suggesting the research question (RQ4): "What is the relative contribution of IS-Impact and IS-Support to Satisfaction?" With the goal of testing the above research questions, IS-Impact, IS-Support and Satisfaction were operationalised in a quantitative survey instrument. Partial least squares (PLS) structural equation modelling employing 221 valid responses largely evidenced the validity of the commencing IS-Impact model in the HR context. ISSupport too was validated as operationalised (including 11 reflective measures of its 4 formative dimensions). IS-Support alone explained 36% of Satisfaction; IS-Impact alone 70%; in combination both explaining 71% with virtually all influence of ISSupport subsumed by IS-Impact. Key study contributions to research include: (1) validation of IS-Impact in the HR context, (2) validation of a newly conceptualised IS-Support construct as important antecedent of Satisfaction, and (3) validation of the redundancy of IS-Support when gauging IS-Impact. The study also makes valuable contributions to practice, the research track and the sponsoring organisation.

Forecasting success on large projects : developing reliable scales to predict multiple perspectives by multiple stakeholders over multiple time frames

Our aim is to develop a set of leading performance indicators to enable managers of large projects to forecast during project execution how various stakeholders will perceive success months or even years into the operation of the output. Large projects have many stakeholders who have different objectives for the project, its output, and the business objectives they will deliver. The output of a large project may have a lifetime that lasts for years, or even decades, and ultimate impacts that go beyond its immediate operation. How different stakeholders perceive success can change with time, and so the project manager needs leading performance indicators that go beyond the traditional triple constraint to forecast how key stakeholders will perceive success months or even years later. In this article, we develop a model for project success that identifies how project stakeholders might perceive success in the months and years following a project. We identify success or failure factors that will facilitate or mitigate against achievement of those success criteria, and a set of potential leading performance indicators that forecast how stakeholders will perceive success during the life of the project's output. We conducted a scale development study with 152 managers of large projects and identified two project success factor scales and seven stakeholder satisfaction scales that can be used by project managers to predict stakeholder satisfaction on projects and so may be used by the managers of large projects for the basis of project control.