Some novel techniques of parameter estimation for the dynamical models in biological systems

Inverse problems based on using experimental data to estimate unknown parameters of a system often arise in biological and chaotic systems. In this paper, we consider parameter estimation in systems biology involving linear and non-linear complex dynamical models, including the Michaelis–Menten enzyme kinetic system, a dynamical model of competence induction in Bacillus subtilis bacteria and a model of feedback bypass in B. subtilis bacteria. We propose some novel techniques for inverse problems. Firstly, we establish an approximation of a non-linear differential algebraic equation that corresponds to the given biological systems. Secondly, we use the Picard contraction mapping, collage methods and numerical integration techniques to convert the parameter estimation into a minimization problem of the parameters. We propose two optimization techniques: a grid approximation method and a modified hybrid Nelder–Mead simplex search and particle swarm optimization (MH-NMSS-PSO) for non-linear parameter estimation. The two techniques are used for parameter estimation in a model of competence induction in B. subtilis bacteria with noisy data. The MH-NMSS-PSO scheme is applied to a dynamical model of competence induction in B. subtilis bacteria based on experimental data and the model for feedback bypass. Numerical results demonstrate the effectiveness of our approach.

Exploring the parameter space of a rabbit ventricular action potential model to investigate the effect of variation on action potential and calcium transients

Computational models for cardiomyocyte action potentials (AP) often make use of a large parameter set. This parameter set can contain some elements that are fitted to experimental data independently of any other element, some elements that are derived concurrently with other elements to match experimental data, and some elements that are derived purely from phenomenological fitting to produce the desired AP output. Furthermore, models can make use of several different data sets, not always derived for the same conditions or even the same species. It is consequently uncertain whether the parameter set for a given model is physiologically accurate. Furthermore, it is only recently that the possibility of degeneracy in parameter values in producing a given simulation output has started to be addressed. In this study, we examine the effects of varying two parameters (the L-type calcium current (I(CaL)) and the delayed rectifier potassium current (I(Ks))) in a computational model of a rabbit ventricular cardiomyocyte AP on both the membrane potential (V(m)) and calcium (Ca(2+)) transient. It will subsequently be determined if there is degeneracy in this model to these parameter values, which will have important implications on the stability of these models to cell-to-cell parameter variation, and also whether the current methodology for generating parameter values is flawed. The accuracy of AP duration (APD) as an indicator of AP shape will also be assessed.

Parameter estimation for a phenomenological model of the cardiac action potential

The action potential (ap) of a cardiac cell is made up of a complex balance of ionic currents which flow across the cell membrane in response to electrical excitation of the cell. Biophysically detailed mathematical models of the ap have grown larger in terms of the variables and parameters required to model new findings in subcellular ionic mechanisms. The fitting of parameters to such models has seen a large degree of parameter and module re-use from earlier models. An alternative method for modelling electrically exciteable cardiac tissue is a phenomenological model, which reconstructs tissue level ap wave behaviour without subcellular details. A new parameter estimation technique to fit the morphology of the ap in a four variable phenomenological model is presented. An approximation of a nonlinear ordinary differential equation model is established that corresponds to the given phenomenological model of the cardiac ap. The parameter estimation problem is converted into a minimisation problem for the unknown parameters. A modified hybrid Nelder–Mead simplex search and particle swarm optimization is then used to solve the minimisation problem for the unknown parameters. The successful fitting of data generated from a well known biophysically detailed model is demonstrated. A successful fit to an experimental ap recording that contains both noise and experimental artefacts is also produced. The parameter estimation method’s ability to fit a complex morphology to a model with substantially more parameters than previously used is established.

Cost efficiency v quality service : using CHAT as a tool for understanding change and transformation in work practices

This chapter provides an analysis of feedback from key stakeholders, collected as part of a research project, on the problems and tensions evident in the collective work practices of learning advisers employed in learning assistance services at an Australian metropolitan university (Peach, 2003). The term 'learning assistance' is used in the Australian higher education sector generally to refer to student support services that include assistance with academic writing and other study skills. The aim of the study was to help learning advisers and other key stakeholders develop a better understanding of the work activity with a view to using this understanding to generate improvements in service provision. Over twenty problems and associated tensions were identified through stakeholder feedback however the focus of this chapter is the analysis of tensions related to a cluster of problems referred to as cost-efficiency versus quality service. Theoretical modelling derived from the tools made available through cultural historical activity theory and expansive visibilsation (Engestrom and Miettinen, 1999) and excerpts from data are used to illustrate how different understandings of the purpose of learning assistance services impacts on the work practices of learning advisers and creates problems and tensions in relation to the type of service available (including use of technology),level of service available, and learning adviser workload.

Social Procurement: Promoting the sustainability of NPOs through the transformation of economic, social and cultural capital

Social procurement provides a key source of income for the Third Sector, and is vital for the sustainability of many nonprofit organisations. Social procurement involves the exchange of economic capital from one organisation, typically government (although for-profit and non-profit organisations can also purchase), with a nonprofit organisations in order to deliver other forms of. It is this transformation of economic capital into other forms of capital (cultural, human, social) in the social procurement process, which is the focus of this paper. Four case studies, which are representative of the four main types of social procurement, will be examined in order to trace how economic capital is transformed into other types of capital in each of these cases. In so doing, the paper will advance our understanding of social procurement theoretically, and lead to a wider discussion about the role of social procurement in ensuring the sustainability of nonprofit organisations, and the civil societies in which they operate.

Towards an orchestration theory in business transformation management (research in progress)

Business transformations are large-scale organisational change projects that, evidence suggests, are often unsuccessful. This study aims to develop a conceptual model that explains how management services that are required for a business transformation are orchestrated during such a initiative. We classify management services such as (but not limited to) change management, risk management, IT management, financial management, program management and so forth as bearing transformational and/or transactional capabilities in a transformation initiative. We then draw upon three principles of musical composition, namely melody, harmony and rhythm, and illustrate how they apply to the orchestration of management services in the management of business transformations. In order to illustrate our emerging model, we examine the case of Malaysia Airlines, who have managed to successfully turnaround the near-bankrupt organisation beyond survival. We demonstrate how the notions of melody, harmony and rhythm can be used to describe their endeavour. We conclude by discussing next steps of our research.

A conceptual model to link deep customer insights to both growth opportunities and organisational strategy in SME’s as part of a design led transformation journey

Although Design Led Innovation activities aim to raise the value of design within the business, knowledge about which tools are available to support companies and how to apply them to make the connection between design for new product development and design as a strategic driver of growth is needed. This paper presents a conceptual method to supplement existing process and tools to assist companies to grow through design. The model extends the authors’ previous work to explore how through storytelling, customer observation can be captured and translated into new meaning, then creating new design propositions shaped into product needs, which can drive internal business activities, brand and the strategic vision. The paper contributes to a gap in the theoretical frameworks and literature by highlighting the need to align and scale design processes which match the needs of SME’s as they transition along a trajectory to become design led businesses.

Can transfer of learning be enriched by valuing knowledge transformation and co-creation? Exploring new ways to improve training design

This paper argues that a possible cause of issues with management education outcomes is the fact that most training models operate from a limited ‘transfer’ metaphor. This theoretical paper contends that by reconceptualising existing models, specifically Holton’s transfer of learning model, to incorporate multiple processes and acknowledge the importance of educator- or trainer-student interaction in co-creating knowledge, there is potential to improve training design and ultimately achieve more satisfactory training outcomes.

Effect of soil parameter uncertainty on seismic response of buried segmented pipeline

Pipelines are important lifeline facilities spread over a large area and they generally encounter a range of seismic hazards and different soil conditions. The seismic response of a buried segmented pipe depends on various parameters such as the type of buried pipe material and joints, end restraint conditions, soil characteristics, burial depths, and earthquake ground motion, etc. This study highlights the effect of the variation of geotechnical properties of the surrounding soil on seismic response of a buried pipeline. The variations of the properties of the surrounding soil along the pipe are described by sampling them from predefined probability distribution. The soil-pipe interaction model is developed in OpenSEES. Nonlinear earthquake time-history analysis is performed to study the effect of soil parameters variability on the response of pipeline. Based on the results, it is found that uncertainty in soil parameters may result in significant response variability of the pipeline.

Leading the transformation of learning and praxis in science classrooms

Individual science teachers who have inspired colleagues to transform their classroom praxis have been labelled transformational leaders. As the notion of distributed leadership became more accepted in the educational literature, the focus on the individual teacher-leader shifted to the study of leadership praxis both by individuals (whoever they might be) and by collectives within schools and science classrooms. This review traces the trajectory of leadership research, in the context of learning and teaching science, from an individual focus to a dialectical relationship between individual and collective praxis. The implications of applying an individual-collective perspective to praxis for teachers, students and their designated leaders are discussed.

Agrobacterium-mediated transformation of indica rice cultivars using binary and superbinary vectors

The Agrobacterium-mediated transformation system was extended to two indica cultivars: a widely cultivated breeding line IR-64 and an elite basmati cultivar Karnal Local. Root tips and shoot tips of seedlings, and scutellar-calli derived from mature seeds showed high-efficiency Agrobacterium tumefaciens infection and stable transformation. In addition to the superbinary vector pTOK233 in Agrobacterium strain LBA4404, almost equally high levels of transformation were achieved with a relatively much smaller (13.1 kb) binary vector (pCAMBIA1301) in a supervirulent host strain AGL1. In both cases, as well as in both cultivars, while 60–90% of the infected explants produced calli resistant to the selectable agent hygromycin, 59–75% of such calli tested positive for GUS. A high level (400 μM) of acetosyringone in the preinduction medium for Agrobacterium and a higher level (500 μM) in the cocultivation medium was necessary for an enhancement in transformation frequency of the binary vector to levels comparable to a superbinary. Hygromycin-resistant calli could be produced from all the explants used. Transformants could be regenerated for both cultivars using the superbinary and binary vector, but only for calli of scutellar origin. In addition to the molecular confirmation of hpt and gus gene transfer and transcription, absence of gene sequences outside the transferred DNA (T-DNA) region confirmed absence of any long T-DNA transfer.

Qualitative inquiry as transformation and agency : the black sheep and workplace mobbing

This chapter discusses an action research project into the lived experience of the workplace mobbing phenomenon. The action research methodology is based on the exemplarian model (Coenen & Khonraad, 2003) from the Netherlands Group. This model requires positive outcomes for those immersed in the problem to reduce the adversity of their circumstances. The findings challenge the psychological perspective of the existing bullying literature that tends to focus on individual behaviour. This research, undertaken over a three year period with 212 participants, identified the dysfunctional nature of public sector bureaucracies and the power gained through gossip and rumour as some of the key emergent themes to explain the workplace mobbing problem. In addition, resistance, conscientisation, and agency were identified as the key to transformation for those targeted. The discussion focuses on the crystallisation phase of the exemplarian model where the participants identified themselves as the Black Sheep and adopted the motto that “a black sheep is a biting beast” (Bastard, 1565 or 6-1618, p. 90), reflecting a sense of empowerment, individual agency, and a sense of humour in dealing with the serious yet seemingly absurd reality of their situations. The identity of the Black Sheep was consolidated when the group organised a 2 day conference with over 200 attendees to discuss how best to prevent workplace mobbing. This self-affirming action was a proactive step towards metaphorically “biting back” at the problem. A number of positive outcomes were achieved including the conference with over 200 attending leading to national media coverage across Australia and additional interviews with magazines, newspapers, and radio.

Development of a transformation system for sorghum (Sorghum bicolor L.)

Sorghum (Sorghum bicolor (L.) Moench) is the world’s fifth major cereal crop and holds importance as a construction material, food and fodder source. More recently, the potential of this plant as a biofuel source has been noted. Despite its agronomic importance, the use of sorghum production is being constrained by both biotic and abiotic factors. These challenges could be addressed by the use of genetic engineering strategies to complement conventional breeding techniques. However, sorghum is one of the most recalcitrant crops for genetic modification with the lack of an efficient tissue culture system being amongst the chief reasons. Therefore, the aim of this study was to develop an efficient tissue culture system for establishing regenerable embryogenic cell lines, micropropagation and acclimatisation for Sorghum bicolor and use this to optimise parameters for genetic transformation via Agrobacterium-mediated transformation and microprojectile bombardment. Using five different sorghum cultivars, SA281, 296B, SC49, Wray and Rio, numerous parameters were investigated in an attempt to establish an efficient and reproducible tissue culture and transformation system. Using immature embryos (IEs) as explants, regenerable embryogenic cell lines (ECLs) could only be established from cultivars SA281 and 296B. Large amounts of phenolics were produced from IEs of cultivars, SC49, Wary and Rio, and these compounds severely hindered callus formation and development. Cultivar SA281 also produced phenolics during regeneration. Attempts to suppress the production of these compounds in cultivars SA281 and SC49 using activated charcoal, PVP, ascorbic acid, citric acid and liquid filter paper bridge methods were either ineffective or had a detrimental effect on embryogenic callus formation, development and regeneration. Immature embryos sourced during summer were found to be far more responsive in vitro than those sourced during winter. In an attempt to overcome this problem, IEs were sourced from sorghum grown under summer conditions in either a temperature controlled glasshouse or a growth chamber. However, the performance of these explants was still inferior to that of natural summer-sourced explants. Leaf whorls, mature embryos, shoot tips and leaf primordia were found to be unsuitable as explants for establishing ECLs in sorghum cultivars SA281 and 296B. Using the florets of immature inflorescences (IFs) as explants, however, ECLs were established and regenerated for these cultivars, as well as for cultivar Tx430, using callus induction media, SCIM, and regeneration media, VWRM. The best in vitro responses, from the largest possible sized IFs, were obtained using plants at the FL-2 stage (where the last fully opened leaf was two leaves away from the flag leaf). Immature inflorescences could be stored at 25oC for up to three days without affecting their in vitro responses. Compared to IEs, the IFs were more robust in tissue culture and showed responses which were season and growth condition independent. A micropropagation protocol for sorghum was developed in this study. The optimum plant growth regulator (PGR) combination for the micropropagation of in vitro regenerated plantlets was found to be 1.0 mg/L BAP in combination with 0.5 mg/L NAA. With this protocol, cultivars 296B and SA281 produced an average of 57 and 13 off-shoots per plantlet, respectively. The plantlets were successfully acclimatised and developed into phenotypically normal plants that set seeds. A simplified acclimatisation protocol for in vitro regenerated plantlets was also developed. This protocol involved deflasking in vitro plantlets with at least 2 fully-opened healthy leaves and at least 3 roots longer than 1.5 cm, washing the media from the roots with running tap water, planting in 100 mm pots and placing in plastic trays covered with a clear plastic bag in a plant growth chamber. After seven days, the corners of the plastic cover were opened and the bags were completely removed after 10 days. All plantlets were successfully acclimatised regardless of whether 1:1 perlite:potting mix, potting mix, UC mix or vermiculite were used as potting substrates. Parameters were optimised for Agrobacterium-mediated transformation (AMT) of cultivars SA281, 296B and Tx430. The optimal conditions were the use of Agrobacterium strain LBA4404 at an inoculum density of 0.5 OD600nm, heat shock at 43oC for 3 min, use of the surfactant Pluronic F-68 (0.02% w/v) in the inoculation media with a pH of 5.2 and a 3 day co-cultivation period in dark at 22oC. Using these parameters, high frequencies of transient GFP expression was observed in IEs precultured on callus initiation media for 1-7 days as well as in four weeks old IE- and IF-derived callus. Cultivar SA281 appeared very sensitive to Agrobacterium since all tissue turned necrotic within two weeks post-exposure. For cultivar 296B, GFP expression was observed up to 20 days post co-cultivation but no stably transformed plants were regenerated. Using cultivar Tx430, GFP was expressed for up to 50 days post co-cultivation. Although no stably transformed plants of this cultivar were regenerated, this was most likely due to the use of unsuitable regeneration media. Parameters were optimised for transformation by particle bombardment (PB) of cultivars SA281, 296B and Tx430. The optimal conditions were use of 3-7 days old IEs and 4 weeks old IF callus, 4 hour pre- and post-bombardment osmoticum treatment, use of 0.6 µm gold microparticles, helium pressure of 1500 kPa and target distance of 15 cm. Using these parameters for PB, transient GFP expression was observed for up to 14, 30 and 50 days for cultivars SA281, 296B and Tx430, respectively. Further, the use of PB resulted in less tissue necrosis compared to AMT for the respective cultivars. Despite the presence of transient GFP expression, no stably transformed plants were regenerated. The establishment of regenerable ECLs and the optimization of AMT and PB parameters in this study provides a platform for future efforts to develop an efficient transformation protocol for sorghum. The development of GM sorghum will be an important step towards improving its agronomic properties as well as its exploitation for biofuel production.

Sensitivity of the NMR density matrix to pulse sequence parameters : a simplified analytic approach

We present a formalism for the analysis of sensitivity of nuclear magnetic resonance pulse sequences to variations of pulse sequence parameters, such as radiofrequency pulses, gradient pulses or evolution delays. The formalism enables the calculation of compact, analytic expressions for the derivatives of the density matrix and the observed signal with respect to the parameters varied. The analysis is based on two constructs computed in the course of modified density-matrix simulations: the error interrogation operators and error commutators. The approach presented is consequently named the Error Commutator Formalism (ECF). It is used to evaluate the sensitivity of the density matrix to parameter variation based on the simulations carried out for the ideal parameters, obviating the need for finite-difference calculations of signal errors. The ECF analysis therefore carries a computational cost comparable to a single density-matrix or product-operator simulation. Its application is illustrated using a number of examples from basic NMR spectroscopy. We show that the strength of the ECF is its ability to provide analytic insights into the propagation of errors through pulse sequences and the behaviour of signal errors under phase cycling. Furthermore, the approach is algorithmic and easily amenable to implementation in the form of a programming code. It is envisaged that it could be incorporated into standard NMR product-operator simulation packages.