On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Process systems modelling and applications in granulation: A review

Granulation is one of the fundamental operations in particulate processing and has a very ancient history and widespread use. Much fundamental particle science has occurred in the last two decades to help understand the underlying phenomena. Yet, until recently the development of granulation systems was mostly based on popular practice. The use of process systems approaches to the integrated understanding of these operations is providing improved insight into the complex nature of the processes. Improved mathematical representations, new solution techniques and the application of the models to industrial processes are yielding better designs, improved optimisation and tighter control of these systems. The parallel development of advanced instrumentation and the use of inferential approaches provide real-time access to system parameters necessary for improvements in operation. The use of advanced models to help develop real-time plant diagnostic systems provides further evidence of the utility of process system approaches to granulation processes. This paper highlights some of those aspects of granulation. (c) 2005 Elsevier Ltd. All rights reserved.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Does pharmacogenomics provide an ethical challenge to the utilisation of cost-effectiveness analysis by public health systems?

Pharmacogenomics promotes an understanding of the genetic basis for differences in efficacy or toxicity of drugs in different individuals. Implementation of the outcomes of pharmacogenomic research into clinical practice presents a number of difficulties for healthcare. This paper aims to highlight one of the Unique ethical challenges which pharmacogenomics presents for the utilisation of cost-effectiveness analysis by public health systems. This paper contends that pharmacogenomics provides a challenge to fundamental principles which underlie most systems for deciding which drugs should be publicly subsidised. Pharmacogenomics brings into focus the conflict between equality and utility in the context of using cost-effectiveness analysis to aid distribution of a limited national drug budget.

Functional-structural plant modelling using a combination of architectural analysis, L-systems and a canonical model of function

This paper presents a new method for producing a functional-structural plant model that simulates response to different growth conditions, yet does not require detailed knowledge of underlying physiology. The example used to present this method is the modelling of the mountain birch tree. This new functional-structural modelling approach is based on linking an L-system representation of the dynamic structure of the plant with a canonical mathematical model of plant function. Growth indicated by the canonical model is allocated to the structural model according to probabilistic growth rules, such as rules for the placement and length of new shoots, which were derived from an analysis of architectural data. The main advantage of the approach is that it is relatively simple compared to the prevalent process-based functional-structural plant models and does not require a detailed understanding of underlying physiological processes, yet it is able to capture important aspects of plant function and adaptability, unlike simple empirical models. This approach, combining canonical modelling, architectural analysis and L-systems, thus fills the important role of providing an intermediate level of abstraction between the two extremes of deeply mechanistic process-based modelling and purely empirical modelling. We also investigated the relative importance of various aspects of this integrated modelling approach by analysing the sensitivity of the standard birch model to a number of variations in its parameters, functions and algorithms. The results show that using light as the sole factor determining the structural location of new growth gives satisfactory results. Including the influence of additional regulating factors made little difference to global characteristics of the emergent architecture. Changing the form of the probability functions and using alternative methods for choosing the sites of new growth also had little effect. (c) 2004 Elsevier B.V. All rights reserved.

Theory of strongly correlated electron systems. II. Including correlation effects into electronic structure calculations

We have previously shown that a division of the f-shell into two subsystems gives a better understanding of the cohesive properties as well the general behavior of lanthanide systems. In this article, we present numerical computations, using the suggested method. We show that the picture is consistent with most experimental data, e.g., the equilibrium volume and electronic structure in general. Compared with standard energy band calculations and calculations based on the self-interaction correction and LIDA + U, the f-(non-f)-mixing interaction is decreased by spectral weights of the many-body states of the f-ion. (c) 2005 Wiley Periodicals, Inc.

Understanding conceptual schemas: exploring the role of application and IS domain knowledge

Although information systems (IS) problem solving involves knowledge of both the IS and application domains, little attention has been paid to the role of application domain knowledge. In this study, which is set in the context of conceptual modeling, we examine the effects of both IS and application domain knowledge on different types of schema understanding tasks: syntactic and semantic comprehension tasks and schema-based problem-solving tasks. Our thesis was that while IS domain knowledge is important in solving all such tasks, the role of application domain knowledge is contingent upon the type of understanding task under investigation. We use the theory of cognitive fit to establish theoretical differences in the role of application domain knowledge among the different types of schema understanding tasks. We hypothesize that application domain knowledge does not influence the solution of syntactic and semantic comprehension tasks for which cognitive fit exists, but does influence the solution of schema-based problem-solving tasks for which cognitive fit does not exist. To assess performance on different types of conceptual schema understanding tasks, we conducted a laboratory experiment in which participants with high- and low-IS domain knowledge responded to two equivalent conceptual schemas that represented high and low levels of application knowledge (familiar and unfamiliar application domains). As expected, we found that IS domain knowledge is important in the solution of all types of conceptual schema understanding tasks in both familiar and unfamiliar applications domains, and that the effect of application domain knowledge is contingent on task type. Our findings for the EER model were similar to those for the ER model. Given the differential effects of application domain knowledge on different types of tasks, this study highlights the importance of considering more than one application domain in designing future studies on conceptual modeling.

Tourism crisis and disasters: Enhancing understanding of system effects

This paper examines the definitions and conceptual foundations of crises and distinguishes between crises and disasters. It takes a systems view of these concepts and uses the perspective of systems as organizational networks to examine implications for tourism managers. A tourism destination is perceived as consisting of a network of interacting organizations. This perspective questions the boundaries that should be used to study crisis and disasters. The paper also discusses the possibility of a crisis having a positive outcome for a destination.

Macromolecular interactions during gelatinisation and retrogradation in starch-whey systems as studied by rapid visco-analyser

Gelatinisation and retrogradation of starch-whey mixtures were studied in water (pH 7) using the Rapid Visco-Analyser (RVA). The starch:whey ratios ranged from 0:100 - 100:0. Wheat starch, and whey protein concentrate (about 80% solids basis) and isolate (about 96% solids basis) were used. Mixtures with whey isolates were generally more viscous than those with whey concentrates, and this was attributed to fewer non-protein milk components in the former. Whey protein concentrates and isolates reduced the peak, trough and final viscosities of the mixtures, but the breakdown and setback ratios of the mixtures were increased. The gelatinisation temperature increased with whey substitutions indicating that whey protein delayed starch gelatinisation. The temperature of fastest viscosity development decreased as the amount of whey was increased. Whey protein isolate generally exercised a lesser effect than the concentrate. At between 40 - 50% whey substitutions, the dominant phase changed from starch to protein irrespective of the source of the whey protein. An additive law poorly defined selected RVA parameters. Both macromolecules interacted to define the viscosity of the mixture, and an exponential model predicted the viscosity better than the additive law. The results obtained in this study are discussed to assist the understanding of extrusion processing of starch-whey systems as models for whey-fortified snack and ready-to-eat foods. Copyright ©2006 The Berkeley Electronic Press. All rights reserved.

Maintaining human agency in the design on context-aware systems: Design games in a dental surgery

This paper describes a series of design games, specifically aimed at exploring shifts in human agency in order to inform the design of context-aware applications. The games focused on understanding information handling issues in dental practice with participants from a university dental school playing an active role in the activities. Participatory design activities help participants to reveal potential implicit technical resources that can be presented explicitly in technologies in order to assist humans in managing their interactions with and amidst technical systems gracefully.

Trait physiology and crop modelling to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. We explore whether a crop growth and development modelling framework can link phenotype complexity to underlying genetic systems in a way that strengthens molecular breeding strategies. We use gene-to-phenotype simulation studies on sorghum to consider the value to marker-assisted selection of intrinsically stable QTLs that might be generated by physiological dissection of complex traits. The consequences on grain yield of genetic variation in four key adaptive traits – phenology, osmotic adjustment, transpiration efficiency, and staygreen – were simulated for a diverse set of environments by placing the known extent of genetic variation in the context of the physiological determinants framework of a crop growth and development model. It was assumed that the three to five genes associated with each trait, had two alleles per locus acting in an additive manner. The effects on average simulated yield, generated by differing combinations of positive alleles for the traits incorporated, varied with environment type. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages with gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies. We simulated a marker-assisted selection (MAS) breeding strategy based on the analyses of gene effects. When marker scores were allocated based on the contribution of gene effects to yield in a single environment, there was a wide divergence in rate of yield gain over all environments with breeding cycle depending on the environment chosen for the QTL analysis. It was suggested that knowledge resulting from trait physiology and modelling would overcome this dependency by identifying stable QTLs. The improved predictive power would increase the utility of the QTLs in MAS. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate QTLs.

Spontaneous combustion and simulation of mine fires and their effects on mine ventilation systems

The structure of a comprehensive research project into mine fires study applying the Ventgraph mine fire simulation software, preplanning of escape scenarios and general interaction with rescue responses is outlined. The project has Australian Coal Association Research Program (ACARP) funding and also relies on substantial mining company site support. This practical input from mine operators is essential and allows the approach to be introduced in the most creditable way. The effort is built around the introduction of fire simulation computer software to the Australian mining industry and the consequent modelling of fire scenarios in selected different mine layouts. Application of the simulation software package to the changing mine layouts requires experience to achieve realistic outcomes. Most Australian mines of size currently use a ventilation network simulation program. Under the project a small subroutine has been written to transfer the input data from the existing mine ventilation network simulation program to ‘Ventgraph’. This has been tested successfully. To understand fire simulation behaviour on the mine ventilation system, it is necessary to understood the possible effects of mine fires on various mine ventilation systems correctly first. Case studies demonstrating the possible effects of fires on some typical Australian coal mine ventilation circuits have been examined. The situation in which there is some gas make at the face and effects with fire have also been developed to emphasise how unstable and dangerous situations may arise. The primary objective of the part of the study described in this paper is to use mine fire simulation software to gain better understanding of how spontaneous combustion initiated fires can interact with the complex ventilation behaviour underground during a substantial fire. It focuses on the simulation of spontaneous combustion sourced heatings that develop into open fires. Further, it examines ventilation behaviour effects of spontaneous combustion initiated pillar fires and examines the difficulties these can be present if a ventilation reversal occurs. It also briefly examines simulation of use of the inertisation to assist in mine recovery. Mine fires are recognised across the world as a major hazard issue. New approaches allowing improvement in understanding their consequences have been developed as an aid in handling this complex area.

A simple electromagnetic model for understanding the operation of a MIMO system

Recent years have witnessed intense research in multiple input multiple output (MIMO) wireless communications systems, which use multiple element antennas (MEA) for signal transmission and reception. In this paper, we have described a novel electromagnetic model to investigate the effect of mutual coupling, inter-element spacing and array geometry on the capacity of MIMO systems. Simulation results have been presented illustrating the application of the proposed model. The presented model concept stems from a hollow waveguide analogue. Using this model other aspects such as richness of scattering environment (spacing and clustering), the effect of hard versus soft scatterers and pin hole effect can be investigated.