A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

Peer state assessment of TxDOT maintenance program and practices : workshop and road rally findings

In an effort to evaluate and improve their practices to ensure the future excellence of the Texas highway system, the Texas Department of Transportation (TxDOT) sought a forum in which experts from other state departments of transportation could share their expertise. Thus, the Peer State Review of TxDOT Maintenance Practices project was organized and conducted for TxDOT by the Center for Transportation Research (CTR) at The University of Texas at Austin. The goal of the project was to conduct a workshop at CTR and in the Austin District that would educate the visiting peers on TxDOT’s maintenance practices and invite their feedback. CTR and TxDOT arranged the participation of the following directors of maintenance: Steve Takigawa, CA; Roy Rissky, KS; Eric Pitts, GA; Jim Carney, MO; Jennifer Brandenburg, NC; and David Bierschbach, WA. One of the means used to capture the peer reviewers’ opinions was a carefully designed booklet of 15 questions. The peers provided TxDOT with written responses to these questions, and the oral comments made during the workshop were also captured. This information was then compiled and summarized in the following report. An examination of the peers’ comments suggests that TxDOT should use a more holistic, statewide approach to funding and planning rather than funding and planning for each district separately. Additionally, the peers stressed the importance of allocating funds based on the actual conditions of the roadways instead of on inventory. The visiting directors of maintenance also recommended continuing and proliferating programs that enhance communication, such as peer review workshops.

The use of semantic priming as a paradigm for the detection of faking on self-report psychological tests

It is recognised that individuals do not always respond honestly when completing psychological tests. One of the foremost issues for research in this area is the inability to detect individuals attempting to fake. While a number of strategies have been identified in faking, a commonality of these strategies is the latent role of long term memory. Seven studies were conducted in order to examine whether it is possible to detect the activation of faking related cognitions using a lexical decision task. Study 1 found that engagement with experiential processing styles predicted the ability to fake successfully, confirming the role of associative processing styles in faking. After identifying appropriate stimuli for the lexical decision task (Studies 2A and 2B), Studies 3 to 5 examined whether a cognitive state of faking could be primed and subsequently identified, using a lexical decision task. Throughout the course of these studies, the experimental methodology was increasingly refined in an attempt to successfully identify the relevant priming mechanisms. The results were consistent and robust throughout the three priming studies: faking good on a personality test primed positive faking related words in the lexical decision tasks. Faking bad, however, did not result in reliable priming of negative faking related cognitions. To more completely address potential issues with the stimuli and the possible role of affective priming, two additional studies were conducted. Studies 6A and 6B revealed that negative faking related words were more arousing than positive faking related words, and that positive faking related words were more abstract than negative faking related words and neutral words. Study 7 examined whether the priming effects evident in the lexical decision tasks occurred as a result of an unintentional mood induction while faking the psychological tests. Results were equivocal in this regard. This program of research aligned the fields of psychological assessment and cognition to inform the preliminary development and validation of a new tool to detect faking. Consequently, an implicit technique to identify attempts to fake good on a psychological test has been identified, using long established and robust cognitive theories in a novel and innovative way. This approach represents a new paradigm for the detection of individuals responding strategically to psychological testing. With continuing development and validation, this technique may have immense utility in the field of psychological assessment.

Preventing injuries on a state-wide basis : researchers and parliamentary committees are partners in turning injury prevention and safety research into practice and policy

Context: Parliamentary committees established in Westminster parliaments, such as Queensland, provide a cross-party structure that enables them to recommend policy and legislative changes that may otherwise be difficult for one party to recommend. The overall parliamentary committee process tends to be more cooperative and less adversarial than the main chamber of parliament and, as a result, this process permits parliamentary committees to make recommendations more on the available research evidence and less on political or party considerations. Objectives: This paper considers the contributions that parliamentary committees in Queensland have made in the past in the areas of road safety, drug use as well as organ and tissue donation. The paper also discusses the importance of researchers actively engaging with parliamentary committees to ensure the best evidence based policy outcomes. Key messages: In the past, parliamentary committees have successfully facilitated important safety changes with many committee recommendations based on research results. In order to maximise the benefits of the parliamentary committee process it is essential that researchers inform committees about their work and become key stakeholders in the inquiry process. Researchers can keep committees informed by making submissions to their inquiries, responding to requests for information and appearing as witnesses at public hearings. Researchers should emphasise the key findings and implications of their research as well as considering the jurisdictional implications and political consequences. It is important that researchers understand the differences between lobbying and providing informed recommendations when interacting with committees. Discussion and conclusions: Parliamentary committees in Queensland have successfully assisted in the introduction of evidence based policy and legislation. In order to present best practice recommendations, committees rely on the evidence presented to them including the results of researchers. Actively engaging with parliamentary committees will help researchers to turn their results into practice with a corresponding decrease in injuries and fatalities. Developing an understanding of parliamentary committees, and the typical inquiry process used by these committees, will help researchers to present their research results in a manner that will encourage the adoption of their ideas by parliamentary committees, the presentation of these results as recommendations within the report and the subsequent enactment of the committee’s recommendations by the government.

State of the art and future challenges for information literacy research

This short paper focuses on strategic issues and important research questions.

Volatile properties of particles emitted by compressed natural gas and diesel buses during steady state and transient driving modes

Volatile properties of particle emissions from four compressed natural gas (CNG) and four diesel buses were investigated under steady state and transient driving modes on a chassis dynamometer. The exhaust was diluted utilising a full-flow continuous volume sampling system and passed through a thermodenuder at controlled temperature. Particle number concentration and size distribution were measured with a condensation particle counter and a scanning mobility particle sizer, respectively. We show that, while almost all the particles emitted by the CNG buses were in the nanoparticle size range, at least 85% and 98% were removed at 100ºC and 250ºC, respectively. Closer analysis of the volatility of particles emitted during transient cycles showed that volatilisation began at around 40°C with the majority occurring by 80°C. Particles produced during hard acceleration from rest exhibited lower volatility than that produced during other times of the cycle. Based on our results and the observation of ash deposits on the walls of the tailpipes, we suggest that these non-volatile particles were composed mostly of ash from lubricating oil. Heating the diesel bus emissions to 100ºC removed ultrafine particle numbers by 69% to 82% when a nucleation mode was present and just 18% when it was not.

State convergence and the effectiveness of time-memory-data tradeoffs

Various time-memory tradeoffs attacks for stream ciphers have been proposed over the years. However, the claimed success of these attacks assumes the initialisation process of the stream cipher is one-to-one. Some stream cipher proposals do not have a one-to-one initialisation process. In this paper, we examine the impact of this on the success of time-memory-data tradeoff attacks. Under the circumstances, some attacks are more successful than previously claimed while others are less. The conditions for both cases are established.

State of Origin : Queensland Crown Leasehold - lessons from New South Wales

Throughout Australia freehold land interests are protected by statutory schemes which grant indefeasibility of title to registered interests. Queensland freehold land interests are protected by Torrens system established by the Land Title Act 1994. However, no such protection exists for Crown land interests. The extent of Queensland occupied under some form of Crown tenure, in excess of 70%, means that Queensland Crown land users are disadvantaged when compared to freehold land users. This article examines the role indefeasibility of title has in protecting interests in Crown land. A comparative analysis is undertaken between Queensland and New South Wales land management frameworks to determine whether interests in crown land are adequately protected in Queensland.

Peer state assessment of TxDOT maintenance program and practices, part II : test section survey findings and recommendations

This paper presents a road survey as part of a workshop conducted by the Texas Department of Transportation (TxDOT) to evaluate and improve the maintenance practices of the Texas highway system. Directors of maintenance from six peer states (California, Kansas, Georgia, Missouri, North Carolina, and Washington) were invited to this 3-day workshop. One of the important parts of this workshop was a Maintenance Test Section Survey (MTSS) to evaluate a number of pre-selected one-mile roadway sections. The workshop schedule allowed half a day to conduct the field survey and 34 sections were evaluated. Each of the evaluators was given a booklet and asked to rate the selected road sections. The goals of the MTSS were to: 1. Assess the threshold level at which maintenance activities are required as perceived by the evaluators from the peer states; 2. Assess the threshold level at which maintenance activities are required as perceived by evaluators from other TxDOT districts; and 3. Perform a pilot evaluation of the MTSS concept. This paper summarizes the information obtained from survey and discusses the major findings based on a statistical analysis of the data and comments from the survey participants.

Peer state assessment of TxDOT maintenance program and practices, part I : workshop findings and recommendations

To assess and improve their practices, and thus ensure the future excellence of the Texas highway system, the Texas Department of Transportation (TxDOT) sought a forum in which experts from other State Departments of Transportation could evaluate the TxDOT maintenance program and practices based on their expertise. To meet this need, a Peer State Review of TxDOT Maintenance Practices project was organized and conducted by the Center for Transportation Research (CTR) at The University of Texas at Austin. CTR researchers, along with TxDOT staff, conducted a workshop to present TxDOT’s maintenance practices to the visiting peer reviewers and invite their feedback. Directors of maintenance from six different states—California, Kansas, Georgia, Missouri, North Carolina, and Washington—participated in the workshop. CTR and TxDOT worked together to design a questionnaire with 15 key questions to capture the peers’ opinions on maintenance program and practices. This paper compiles and summarizes this information. The examination results suggested that TxDOT should use a more state-wide approach to funding and planning, in addition to funding and planning for each district separately. Additionally, the peers recommended that criteria such as condition and level of service of the roadways be given greater weight in the funding allocation than lane miles or vehicle miles traveled (VMT). The Peer Reviewers also determined that TxDOT maintenance employee experience and communications were strong assets. Additional strengths included the willingness of TxDOT to invite peer reviews of their practices and a willingness to consider opportunities for improvement.

State convergence in the initialisation of the Sfinks stream cipher

Sfinks is a shift register based stream cipher designed for hardware implementation. The initialisation state update function is different from the state update function used for keystream generation. We demonstrate state convergence during the initialisation process, even though the individual components used in the initialisation are one-to-one. However, the combination of these components is not one-to-one.

Current state of the application of infrared optical methods for assessing articular cartilage

This paper reviews the current state in the application of infrared methods, particularly mid-infrared (mid-IR) and near infrared (NIR), for the evaluation of the structural and functional integrity of articular cartilage. It is noted that while a considerable amount of research has been conducted with respect to tissue characterization using mid-IR, it is almost certain that full-thickness cartilage assessment is not feasible with this method. On the contrary, the relatively more considerable penetration capacity of NIR suggests that it is a suitable candidate for full-thickness cartilage evaluation. Nevertheless, significant research is still required to improve the specificity and clinical applicability of the method if we are going to be able to use it for distinguishing between functional and dysfunctional cartilage.