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.

Evolving genetic regulatory networks performing as stochastic switches

Recent studies have shown that small genetic regulatory networks (GRNs) can be evolved in silico displaying certain dynamics in the underlying mathematical model. It is expected that evolutionary approaches can help to gain a better understanding of biological design principles and assist in the engineering of genetic networks. To take the stochastic nature of GRNs into account, our evolutionary approach models GRNs as biochemical reaction networks based on simple enzyme kinetics and simulates them by using Gillespie’s stochastic simulation algorithm (SSA). We have already demonstrated the relevance of considering intrinsic stochasticity by evolving GRNs that show oscillatory dynamics in the SSA but not in the ODE regime. Here, we present and discuss first results in the evolution of GRNs performing as stochastic switches.

Nanostructured mesoporous bioglass coated zirconia scaffolds for bone tissue engineering

For the filling and reconstruction of non-healing bone defects, the application of porous ceramic scaffold as bone substitutes is considered to be a reasonable choice. In bone tissue engineering, an ideal scaffold must satisfy several criterias such as open porosity, having high compressive strength (it depends where in body, and if external fixatures are used) and the practicability for cell migration. Many researchers have focused on enhancing the mechanical properties of hydroxyapatite scaffolds by combining it with other biomaterials, such as bioglass and polymers. Nevertheless, there is still a lack of suitable scaffolds based on porous biomaterials. In this study, zirconia scaffolds from two different templates (polyurethane (PU) and Acrylonitrile Butadiene Styrene (ABS) templates) were successfully fabricated with dissimilar fabrication techniques. The scaffold surfaces were further modified with mesoporous bioglass for the purpose of bone tissue engineering. In the study of PU template scaffold, high porosity (~88%) sol-gel derived yttria-stabilized zirconia (YSZ) scaffold was prepared by a polyurethane (PU) foam replica method using sol-gel derived zirconia for the first time, and double coated with Mesoporous Bioglass (MBGs) coating. For the ABS template scaffold, two types of templates (cube and cylinder) with different strut spacings were used and fabricated by a 3D Rapid Prototyper. Subsequently, zirconia scaffolds with low porosity (63±2.8% to 68±2.5%) were fabricated by embedding the zirconia powder slurry into the ABS templates and burning out the ABS to produce a uniform porous structure. The zirconia scaffolds were double coated with mesoporous bioglass by dip coating for the first time. The porosities of the scaffolds were calculated before and after coating. The microstructures were then examined using scanning electron microscopy and the mechanical properties were evaluated using compressive test. Accordingly, relationships between microstructure, processing and mechanical behaviour of the porous zirconia was discussed. Scaffold biocompatibility and bioactivity was also evaluated using a bone marrow stromal cell (BMSC) proliferation test and a simulated body fluid test.

Preparation and characterisation of tri-calcium phosphate scaffolds with tunnel-like macro-pores for bone tissue engineering

Calcium Phosphate ceramics have been widely used in tissue engineering due to their excellent biocompatibility and biodegradability. In the physiological environment, they are able to gradually degrade, absorbed and promote bone growth. Ultimately, they are capable of replacing damaged bone with new tissue. However, their low mechanical properties limit calcium phosphate ceramics in load-bearing applications. To obtain sufficient mechanical properties as well as high biocompatibility is one of the main focuses in biomaterials research. Therefore, the current project focuses on the preparation and characterization of porous tri-calcium phosphate (TCP) ceramic scaffolds. Hydroxapatite (HA) was used as the raw material, and normal calcium phosphate bioglass was added to adjust the ratio between calcium and phosphate. It was found that when 20% bioglass was added to HA and sintered at 1400oC for 3 hours, the TCP scaffold was obtained and this was confirmed by X-ray diffraction (XRD) analysis. Test results have shown that by applying this method, TCP scaffolds have significantly higher compressive strength (9.98MPa) than those made via TCP powder (<3MPa). Moreover, in order to further increase the compressive strength of TCP scaffolds, the samples were then coated with bioglass. For normal bioglass coated TCP scaffold, compressive strength was 16.69±0.5MPa; the compressive strength for single layer mesoporous bioglass coated scaffolds was 15.03±0.63MPa. In addition, this project has also concentrated on sizes and shapes effects; it was found that the cylinder scaffolds have more mechanical property than the club ones. In addition, this project performed cell culture within scaffold to assess biocompatibility. The cells were well distributed in the scaffold, and the cytotoxicity test was performed by 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di- phenytetrazoliumromide (MTT) assay. The Alkaline Phosphatase (Alp) activity of human bone marrow mesenchymal stem cell system (hBMSCs) seeded on scaffold expressed higher in vitro than that in the positive control groups in osteogenic medium, which indicated that the scaffolds were both osteoconductive and osteoinductive, showing potential value in bone tissue engineering.

Teaching motor racing engineering through real-life projects: benefits and challenges

Project-based learning (PBL) is widely used in engineering courses. The closer to real-life the project, the greater the relevance and depth of learning experienced by students. Formula Society of Automotive Engineering (FSAE) is a fine example of a team-based project modelled on real-life problems whereby each student team designs and builds a small race car for competitive evaluation. Queensland University of Technology (QUT) has participated in FSAE-Australia since 2004. Based on the success of the project, QUT has gone the additional step of introducing a motor-racing specialization (second major) to complement its mechanical engineering degree. In this paper, the benefits of teaching motor-racing engineering through real-life projects are presented together with a discussion of the challenges faced and how they have been addressed. In order to validate the authors' observations on the teaching approaches used, student feedback was solicited through QUT's online learning experience survey (LEX), as well as a customized paper-based survey. The results of the surveys are analysed and discussed in this paper.

Efficient hybrid-game strategies coupled to evolutionary algorithms for robust multidisciplinary design optimization in aerospace engineering

A number of game strategies have been developed in past decades and used in the fields of economics, engineering, computer science, and biology due to their efficiency in solving design optimization problems. In addition, research in multiobjective and multidisciplinary design optimization has focused on developing a robust and efficient optimization method so it can produce a set of high quality solutions with less computational time. In this paper, two optimization techniques are considered; the first optimization method uses multifidelity hierarchical Pareto-optimality. The second optimization method uses the combination of game strategies Nash-equilibrium and Pareto-optimality. This paper shows how game strategies can be coupled to multiobjective evolutionary algorithms and robust design techniques to produce a set of high quality solutions. Numerical results obtained from both optimization methods are compared in terms of computational expense and model quality. The benefits of using Hybrid and non-Hybrid-Game strategies are demonstrated.

Management and engineering of process aware information systems : introduction to the special issue

In this editorial letter, we provide the readers of Information Systems with a birds-eye introduction to Process-aware Information Systems (PAIS) – a sub-field of Information Systems that has drawn growing attention in the past two decades, both as an engineering and as a management discipline. Against this backdrop, we briefly discuss how the papers included in this special issue contribute to extending the body of knowledge in this field.

Effects of varied ionic calcium and phosphate on the proliferation, osteogenic differentiation and mineralization of human periodontal ligament cells in vitro

Background and Objective: A number of bone filling materials containing calcium (Ca++) and phosphate (P) ions have been used in the repair of periodontal bone defects; however, the effect that local release of Ca++ and P ions have on biological reactions is not fully understood. In this study, we investigated the effects of various levels of Ca++ and P ions on the proliferation, osteogenic differentiation, and mineralization of human periodontal ligament cells (hPDLCs). Materials and Methods: hPDLCs were obtained using an explant culture method. Defined concentrations and ratios of ionic Ca++ to inorganic P were added to standard culture and osteogenic induction media. The ability of hPDLCs to proliferate in these growth media was assayed using the Cell Counting Kit-8 (CCK-8). Cell apoptosis was evaluated by FITC-Annexin V/PI double staining method. Osteogenic differentiation and mineralization were investigated by morphological observations, alkaline phosphatase (ALP) activity, and Alizarin red S/von Kossa staining. The mRNA expression of osteogenic related markers was analyzed using a reverse transcriptase polymerase chain reaction (RT-PCR). Results: Within the ranges of Ca++ and P ions concentrations tested, we observed that increased concentrations of Ca++ and P ions enhanced cell proliferation and formation of mineralized matrix nodules; whereas ALP activity was reduced. The RT-PCR results showed that elevated concentrations of Ca++ and P ions led to a general increase of Runx2 mRNA expression and decreased ALP mRNA expression, but gave no clear trend on OCN mRNA levels. Conclusion: The concentrations and ratios of Ca++ and P ions could significantly influence proliferation, differentiation, and mineralization of hPDLCs. Within the range of concentrations tested, we found that the combination of 9.0 mM Ca++ ions and 4.5 mM P ions were the optimum concentrations for proliferation, differentiation, and mineralization in hPDLCs.

A review of optimization techniques used in the design of fibre composite structures for civil engineering applications

Fibre composite structures have become the most attractive candidate for civil engineering applications. Fibre reinforced plastic polymer (FRP) composite materials have been used in the rehabilitation and replacement of the old degrading traditional structures or build new structures. However, the lack of design standards for civil infrastructure limits their structural applications. The majority of the existing applications have been designed based on the research and guidelines provided by the fibre composite manufacturers or based on the designer’s experience. It has been a tendency that the final structure is generally over-designed. This paper provides a review on the available studies related to the design optimization of fibre composite structures used in civil engineering such as; plate, beam, box beam, sandwich panel, bridge girder, and bridge deck. Various optimization methods are presented and compared. In addition, the importance of using the appropriate optimization technique is discussed. An improved methodology, which considering experimental testing, numerical modelling, and design constrains, is proposed in the paper for design optimization of composite structures.

Relationship management as a strategy for supply chain engagement in the civil engineering construction industry

Many studies into construction procurement methods reveal evidence of a need to change the culture and attitude in the construction industry, transition from traditional adversarial relationships to cooperative and collaborative relationships. At the same time there is also increasing concern and discussion on alternative procurement methods, involving a movement away from traditional procurement systems. Relational contracting approaches, such as partnering and relationship management, are business strategies that align the objectives of clients, commercial participants and stakeholders. It provides a collaborative environment and a framework for all participants to adapt their behaviour to project objectives and allows for engagement of those subcontractors and suppliers down the supply chain. The efficacy of relationship management in the client and contractor groups is proven and well documented. However, the industry has a history of slow implementation of relational contracting down the supply chain. Furthermore, there exists little research on relationship management conducted in the supply chain context. This research aims to explore the association between relational contracting structures and processes and supply chain sustainability in the civil engineering construction industry. It endeavours to shed light on the practices and prerequisites for relationship management implementation success and for supply sustainability to develop. The research methodology is a triangulated approach based on Cheung.s (2006) earlier research where questionnaire survey, interviews and case studies were conducted. This new research includes a face-to-face questionnaire survey that was carried out with 100 professionals from 27 contracting organisations in Queensland from June 2008 to January 2009. A follow-up survey sub-questionnaire, further examining project participants. perspectives was sent to another group of professionals (as identified in the main questionnaire survey). Statistical analysis including multiple regression, correlation, principal component factor analysis and analysis of variance were used to identify the underlying dimensions and test the relationships among variables. Interviews and case studies were conducted to assist in providing a deeper understanding as well as explaining findings of the quantitative study. The qualitative approaches also gave the opportunity to critique and validate the research findings. This research presents the implementation of relationship management from the contractor.s perspective. Findings show that the adaption of relational contracting approach in the supply chain is found to be limited; contractors still prefer to keep the suppliers and subcontractors at arm.s length. This research shows that the degree of match and mismatch between organisational structuring and organisational process has an impact on staff.s commitment level and performance effectiveness. Key issues affecting performance effectiveness and relationship effectiveness include total influence between parties, access to information, personal acquaintance, communication process, risk identification, timely problem solving and commercial framework. Findings also indicate that alliance and Early Contractor Involvement (ECI) projects achieve higher performance effectiveness at both short-term and long-term levels compared to projects with either no or partial relationship management adopted.

Spatial/surveying programs repositioning within new STEM Faculty at QUT

Many of the undergraduate and postgraduate programs of the former Faculty of Built Environment and Engineering PLUS Faculty of Sciences and Technology are changing as a result of merging these two large organisations, with some disciplines relocating to faculties of Creative Industries and Health respectively. The new STEM precinct under construction has begun rising from the proverbial hole-in-the-ground. Existing Surveying and Spatial Sciences programs, assets and staff are being repositioned with the newly formed School of Earth, Environment and Biological Sciences.2011. Golden graduates morning tea organised by QUT Alumni. Technology upgrades to the Mapping Sciences lab benefits 3-D learning experiences. Second and third-year students are undertaking Work Integrated Learning (WIL) over the summer vacation period. Final year students recently presented capstone project presentations at mini-conference in the Gibson Rooms overlooking a vibrant Southbank and sparkling Brisbane River. Discussion on end of year graduation ceremony held at QPAC.

Temporal tracking of mineralization and transcriptional developments of shell formation during the early life history of pearl oyster Pinctada maxima

Molluscan larval ontogeny is a highly conserved process comprising three principal developmental stages. A characteristic unique to each of these stages is shell design, termed prodissoconch I, prodissoconch II and dissoconch. These shells vary in morphology, mineralogy and microstructure. The discrete temporal transitions in shell biomineralization between these larval stages are utilized in this study to investigate transcriptional involvement in several distinct biomineralization events. Scanning electron microscopy and X-ray diffraction analysis of P. maxima larvae and juveniles collected throughout post-embryonic ontogenesis, document the mineralogy and microstructure of each shelled stage as well as establishing a timeline for transitions in biomineralization. P. maxima larval samples most representative of these biomineralization distinctions and transitions were analyzed for differential gene expression on the microarray platform PmaxArray 1.0. A number of transcripts are reported as differentially expressed in correlation to the mineralization events of P. maxima larval ontogeny. Some of those isolated are known shell matrix genes while others are novel; these are discussed in relation to potential shell formation roles. This interdisciplinary investigation has linked the shell developments of P. maxima larval ontogeny with corresponding gene expression profiles, furthering the elucidation of shell biomineralization.

Engineering-based modelling experiences in the elementary classroom

Introducing engineering-based model-eliciting experiences in the elementary curriculum is a new and increasingly important domain of research by mathematics, science, technology, and engineering educators. Recent research has raised questions about the context of engineering problems that are meaningful, engaging, and inspiring for young students. In the present study an environmental engineering activity was implemented in two classes of 11-year-old students in Cyprus. The problem required students to develop a procedure for selecting among alternative countries from which to buy water. Students created a range of models that adequately solved the problem although not all models took into account all of the data provided. The models varied in the number of problem factors taken into consideration and also in the different approaches adopted in dealing with the problem factors. At least two groups of students integrated into their models the environmental aspect of the problem (energy consumption, water pollution) and further refined their models. Results indicate that engineering model-eliciting activities can be introduced effectively into the elementary curriculum, providing rich opportunities for students to deal with engineering contexts and to apply their learning in mathematics and science to solving real-world engineering problems.