Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

A traffic simulation standard based on data marts

Traffic Simulation models tend to have their own data input and output formats. In an effort to standardise the input for traffic simulations, we introduce in this paper a set of data marts that aim to serve as a common interface between the necessaary data, stored in dedicated databases, and the swoftware packages, that require the input in a certain format. The data marts are developed based on real world objects (e.g. roads, traffic lights, controllers) rather than abstract models and hence contain all necessary information that can be transformed by the importing software package to their needs. The paper contains a full description of the data marts for network coding, simulation results, and scenario management, which have been discussed with industry partners to ensure sustainability.

Integrating treatment for mental and physical disorders and substance misuse in Indigenous primary care settings

Objective: Australian Indigenous peoples in remote and rural settings continue to have limited access to treatment for mental illness. Comorbid disorders complicate presentations in primary care where Indigenous youths and perinatal women are at particular risk. Despite this high comorbidity there are few examples of successful models of integrated treatment. This paper outlines these challenges and provides recommendations for practice that derive from recent developments in the Northern Territory. Conclusions: There is a strong need to develop evidence for the effectiveness of integrated and culturally informed individual and service level interventions. We describe the Best practice in Early intervention Assessment and Treatment of depression and substance misuse study which seeks to address this need.

Which older women could benefit from interventions to decrease sitting time and increase physical activity?

In addition to the well-known health risks associated with lack of physical activity (PA), evidence is emerging about the health risks of sedentary behaviour (sitting). Research about patterns and correlates of sitting and PA in older women is scarce. METHODS: Self-report data from 6,116 women aged 76-81 years were collected as part of the Australian Longitudinal Study on Woman’s Health. Linear regression models were computed to examine whether demographic, social and health factors were associated with sitting and PA. RESULTS: Women who did no PA sat more than women who did any PA (p<0.001). Seven correlates were associated with sitting and PA (p<0.05). Five of these were associated with more sitting and less PA: three health-related (BMI, chronic conditions, anxiety/depression) and two social correlates (caring duties, volunteering). One demographic (being from another English-speaking country) and one social correlate (more social interaction) were associated with more sitting and more PA. Four correlates, two demographic (living in a city; post-high school education), one social (being single), and one health-related correlate (dizziness/loss of balance) were associated with more sitting only. Two other health-related correlates (stiff/painful joints; feet problems) were associated with less PA only. CONCLUSION: Sedentary behaviour and PA are distinct behaviours in older Australian women. Information about the correlates of both behaviours can be used to identify population groups who might benefit from interventions to reduce sedentary behaviour and/or increase PA.

Modelling contractor's and subcontractor's trust : a system dynamics approach

A general mistrust within the contactor and subcontractor companies has identified one of the significant barriers to derive benefits from true downstream supply chain integration. Using the general theory of trust in inter-organizational relations and conducting interviews, this research discusses factors that influence development of trust and cooperation in contractor– subcontractor relationships in construction projects. System dynamics is the simulation method is selected in this theory-building effort, based on qualitative data collected from two projects of a construction company in Thailand. Performance, permeability and system based trust are found to make significant contributions toward parties’ trust level. Three strategic policies such as best value contracting, management of subcontractors as internal team and semi project partnering approach are recommended to stimulate the trust factors as well as cooperative long term relationship.

Influence of physical and chemical parameters on the treatment of heavy metals in polluted stormwater using zeolite : A review

Zeolite-based technology can provide a cost effective solution for stormwater treatment for the removal of toxic heavy metals under increasing demand of safe water from alternative sources. This paper reviews the currently available knowledge relating to the effect of properties of zeolites such as pore size, surface area and Si:Al ratio and the physico-chemical conditions of the system such as pH, temperature, initial metal concentration and zeolite concentration on heavy metal removal performance. The primary aims are, to consolidate available knowledge and identify knowledge gaps. It was established that an in-depth understanding of operational issues such as, diffusion of metal ions into the zeolite pore structure, pore clogging, zeolite surface coverage by particulates in stormwater as well as the effect of pH on stormwater quality in the presence of zeolites is essential for developing a zeolite-based technology for the treatment of polluted stormwater. The optimum zeolite concentration to treat typical volumes of stormwater and initial heavy metal concentrations in stormwater should also be considered as operational issues in this regard. Additionally, leaching of aluminium and sodium ions from the zeolite structure to solution were identified as key issues requiring further research in the effort to develop cost effective solutions for the removal of heavy metals from stormwater.

Bilski v Kappos : The United States Supreme Court delivers mixed views on patenting non-physical inventions and business methods

The United States Supreme Court has handed down a once in a generation patent law decision that will have important ramifications for the patentability of non-physical methods, both internationally and in Australia. In Bilski v Kappos, the Supreme Court considered whether an invention must either be tied to a machine or apparatus, or transform an article into a different state or thing to be patentable. It also considered for the first time whether business methods are patentable subject matter. The decision will be of particular interest to practitioners who followed the litigation in Grant v Commissioner of Patents, a Federal Court decision in which a Brisbane-based inventor was denied a patent over a method of protecting an asset from the claims of creditors.

A study of abrasive water jet characteristics by CFD simulation

Computational fluid dynamics (CFD) models for ultrahigh velocity waterjets and abrasive waterjets (AWJs) are established using the Fluent 6 flow solver. Jet dynamic characteristics for the flow downstream from a very fine nozzle are then simulated under steady state, turbulent, two-phase and three-phase flow conditions. Water and particle velocities in a jet are obtained under different input and boundary conditions to provide an insight into the jet characteristics and a fundamental understanding of the kerf formation process in AWJ cutting. For the range of downstream distances considered, the results indicate that a jet is characterised by an initial rapid decay of the axial velocity at the jet centre while the cross-sectional flow evolves towards a top-hat profile downstream.

High fidelity simulation; challenges encountered in developing and implementing student learning experiences, staff education and researching approaches to learning

High fidelity simulation as a teaching and learning approach is being embraced by many schools of nursing. Our school embarked on integrating high fidelity (HF) simulation into the undergraduate clinical education program in 2011. Low and medium fidelity simulation has been used for many years, but this did not simplify the integration of HF simulation. Alongside considerations of how and where HF simulation would be integrated, issues arose with: student consent and participation for observed activities; data management of video files; staff development, and conceptualising how methods for student learning could be researched. Simulation for undergraduate student nurses commenced as a formative learning activity, undertaken in groups of eight, where four students undertake the ‘doing’ role and four are structured observers, who then take a formal role in the simulation debrief. Challenges for integrating simulation into student learning included conceptualising and developing scenarios to trigger students’ decision making and application of skills, knowledge and attitudes explicit to solving clinical ‘problems’. Developing and planning scenarios for students to ‘try out’ skills and make decisions for problem solving lay beyond choosing pre-existing scenarios inbuilt with the software. The supplied scenarios were not concept based but rather knowledge, skills and technology (of the manikin) focussed. Challenges lay in using the technology for the purpose of building conceptual mastery rather than using technology simply because it was available. As we integrated use of HF simulation into the final year of the program, focus was on building skills, knowledge and attitudes that went beyond technical skill, and provided an opportunity to bridge the gap with theory-based knowledge that students often found difficult to link to clinical reality. We wished to provide opportunities to develop experiential knowledge based on application and clinical reasoning processes in team environments where problems are encountered, and to solve them, the nurse must show leadership and direction. Other challenges included students consenting for simulations to be videotaped and ethical considerations of this. For example if one student in a group of eight did not consent, did this mean they missed the opportunity to undertake simulation, or that others in the group may be disadvantaged by being unable to review their performance. This has implications for freely given consent but also for equity of access to learning opportunities for students who wished to be taped and those who did not. Alongside this issue were the details behind data management, storage and access. Developing staff with varying levels of computer skills to use software and undertake a different approach to being the ‘teacher’ required innovation where we took an experiential approach. Considering explicit learning approaches to be trialled for learning was not a difficult proposition, but considering how to enact this as research with issues of blinding, timetabling of blinded groups, and reducing bias for testing results of different learning approaches along with gaining ethical approval was problematic. This presentation presents examples of these challenges and how we overcame them.

Using ‘think aloud’ as a strategy for learning clinical reasoning in high fidelity case-based simulation for undergraduate nursing students

AIMS This paper reports on the implementation of a research project that trials an educational strategy implemented over six months of an undergraduate third year nursing curriculum. This project aims to explore the effectiveness of ‘think aloud’ as a strategy for learning clinical reasoning for students in simulated clinical settings. BACKGROUND Nurses are required to apply and utilise critical thinking skills to enable clinical reasoning and problem solving in the clinical setting [1]. Nursing students are expected to develop and display clinical reasoning skills in practice, but may struggle articulating reasons behind decisions about patient care. For students learning to manage complex clinical situations, teaching approaches are required that make these instinctive cognitive processes explicit and clear [2-5]. In line with professional expectations, nursing students in third year at Queensland University of Technology (QUT) are expected to display clinical reasoning skills in practice. This can be a complex proposition for students in practice situations, particularly as the degree of uncertainty or decision complexity increases [6-7]. The ‘think aloud’ approach is an innovative learning/teaching method which can create an environment suitable for developing clinical reasoning skills in students [4, 8]. This project aims to use the ‘think aloud’ strategy within a simulation context to provide a safe learning environment in which third year students are assisted to uncover cognitive approaches that best assist them to make effective patient care decisions, and improve their confidence, clinical reasoning and active critical reflection on their practice. MEHODS In semester 2 2011 at QUT, third year nursing students will undertake high fidelity simulation, some for the first time commencing in September of 2011. There will be two cohorts for strategy implementation (group 1= use think aloud as a strategy within the simulation, group 2= not given a specific strategy outside of nursing assessment frameworks) in relation to problem solving patient needs. Students will be briefed about the scenario, given a nursing handover, placed into a simulation group and an observer group, and the facilitator/teacher will run the simulation from a control room, and not have contact (as a ‘teacher’) with students during the simulation. Then debriefing will occur as a whole group outside of the simulation room where the session can be reviewed on screen. The think aloud strategy will be described to students in their pre-simulation briefing and allow for clarification of this strategy at this time. All other aspects of the simulations remain the same, (resources, suggested nursing assessment frameworks, simulation session duration, size of simulation teams, preparatory materials). RESULTS Methodology of the project and the challenges of implementation will be the focus of this presentation. This will include ethical considerations in designing the project, recruitment of students and implementation of a voluntary research project within a busy educational curriculum which in third year targets 669 students over two campuses. CONCLUSIONS In an environment of increasingly constrained clinical placement opportunities, exploration of alternate strategies to improve critical thinking skills and develop clinical reasoning and problem solving for nursing students is imperative in preparing nurses to respond to changing patient needs. References 1. Lasater, K., High-fidelity simulation and the development of clinical judgement: students' experiences. Journal of Nursing Education, 2007. 46(6): p. 269-276. 2. Lapkin, S., et al., Effectiveness of patient simulation manikins in teaching clinical reasoning skills to undergraduate nursing students: a systematic review. Clinical Simulation in Nursing, 2010. 6(6): p. e207-22. 3. Kaddoura, M.P.C.M.S.N.R.N., New Graduate Nurses' Perceptions of the Effects of Clinical Simulation on Their Critical Thinking, Learning, and Confidence. The Journal of Continuing Education in Nursing, 2010. 41(11): p. 506. 4. Banning, M., The think aloud approach as an educational tool to develop and assess clinical reasoning in undergraduate students. Nurse Education Today, 2008. 28: p. 8-14. 5. Porter-O'Grady, T., Profound change:21st century nursing. Nursing Outlook, 2001. 49(4): p. 182-186. 6. Andersson, A.K., M. Omberg, and M. Svedlund, Triage in the emergency department-a qualitative study of the factors which nurses consider when making decisions. Nursing in Critical Care, 2006. 11(3): p. 136-145. 7. O'Neill, E.S., N.M. Dluhy, and C. Chin, Modelling novice clinical reasoning for a computerized decision support system. Journal of Advanced Nursing, 2005. 49(1): p. 68-77. 8. Lee, J.E. and N. Ryan-Wenger, The "Think Aloud" seminar for teaching clinical reasoning: a case study of a child with pharyngitis. J Pediatr Health Care, 1997. 11(3): p. 101-10.

How design of the physical environment impacts early learning : educators and parents perspectives

This research explores the quality and importance of the physical environment of two early learning centres on the Sunshine Coast in Queensland, utilising qualitative interviews with parents (n=4) and educators (n=4) to understand how design might impact on children’s development and a quantitative rating (the Early Childhood Physical Environment Rating Scale; ECPERS) to assess the quality of the physical built environment and infrastructure. With an average ECPERS quality rating, thematic analysis of the interviews revealed that educators and parents viewed the physical environment as important to a child’s development, although the quality of staff was predominant. Early learning centres should be ‘homely’, inviting, bright and linked to the outdoors, with participants describing how space “welcomes the child, makes them feel safe and encourages learning”. Four key themes characterised views: Emotional Connection (quality of staff and physical environment), Experiencing Design (impact of design on child development), Hub for Community Integration (relationships and resources) and Future Vision (ideal physical environment, technology and ratings). With participants often struggling to clearly articulate their thoughts on design issues, a collaborative and jargon-free approach to designing space is required. These findings will help facilitate discussion about the role and design of the physical environment in early childhood centres, with the tangible examples of ‘ideal space’ enhancing communication between architects and educators about how best to design and reconfigure space to enhance learning outcomes.