Rice morphogenesis and plant architecture: Measurement, specification and the reconstruction of structural development by 3D architectural modelling

Background and Aims The morphogenesis and architecture of a rice plant, Oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3D measurement. The architecture of rice plants is characterized by a large number of tillers and leaves. The aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3D growth across all growth stages. Methods A japonica type rice, 'Namaga', was grown in pots under outdoor conditions. A 3D digitizer was used to measure the rice plant structure at intervals from the young seedling stage to maturity. The L-system formalism was applied to create '3D virtual rice' plants, incorporating models of phenological development and leaf emergence period as a function of temperature and photoperiod, which were used to determine the timing of tiller emergence. Key Results The relationships between the nodal positions and leaf lengths, leaf angles and tiller angles were analysed and used to determine growth functions for the models. The '3D virtual rice' reproduces the structural development of isolated plants and provides a good estimation of the fillering process, and of the accumulation of leaves. Conclusions The results indicated that the '3D virtual rice' has a possibility to demonstrate the differences in the structure and development between cultivars and under different environmental conditions. Future work, necessary to reflect both cultivar and environmental effects on the model performance, and to link with physiological models, is proposed in the discussion.

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.

A distributed systems approach to secure Internet mail

One of the obstacles to improved security of the Internet is ad hoc development of technologies with different design goals and different security goals. This paper proposes reconceptualizing the Internet as a secure distributed system, focusing specifically on the application layer. The notion is to redesign specific functionality, based on principles discovered in research on distributed systems in the decades since the initial development of the Internet. Because of the problems in retrofitting new technology across millions of clients and servers, any options with prospects of success must support backward compatibility. This paper outlines a possible new architecture for internet-based mail which would replace existing protocols by a more secure framework. To maintain backward compatibility, initial implementation could offer a web browser-based front end but the longer-term approach would be to implement the system using appropriate models of replication. (C) 2005 Elsevier Ltd. All rights reserved.

The dendritic architecture of the cholinergic plexus in the rabbit retina: Selective labeling by glycine accumulation in the presence of sarcosine

The cholinergic amacrine cells in the rabbit retina slowly accumulate glycine to very high levels when the tissue is incubated with excess sarcosine (methylglycine), even though these cells do not normally contain elevated levels of glycine and do not express high-affinity glycine transporters. Because the sarcosine also depletes the endogenous glycine in the glycine-containing amacrine cells and bipolar cells, the cholinergic amacrine cells can be selectively labeled by glycine immunocytochemistry under these conditions. Incubation experiments indicated that the effect of sarcosine on the cholinergic amacrine cells is indirect: sarcosine raises the extracellular concentration of glycine by blocking its re-uptake by the glycinergic amacrine cells, and the excess glycine is probably taken-up by an unidentified low-affinity transporter on the cholinergic amacrine cells. Neurobiotin injection of the On-Off direction-selective (DS) ganglion cells in sarcosine-incubated rabbit retina was combined with glycine immunocytochemistry to examine the dendritic relationships between the DS ganglion cells and the cholinergic amacrine cells. These double-labeled preparations showed that the dendrites of the DS ganglion cells closely follow the fasciculated dendrites of the cholinergic amacrine cells. Each ganglion cell dendrite located within the cholinergic strata is associated with a cholinergic fascicle and, conversely, there are few cholinergic fascicles that do not contain at least one dendrite from an On-Off DS cell. It is not known how the dendritic co-fasciculation develops, but the cholinergic dendritic plexus may provide the initial scaffold, because the dendrites of the On-Off DS cells commonly run along the outside of the cholinergic fascicles. J. Comp. Neurol. 421:1-13, 2000. (C) 2000 Wiley-Liss, Inc.

Patterns in complex systems modeling

The design, development, and use of complex systems models raises a unique class of challenges and potential pitfalls, many of which are commonly recurring problems. Over time, researchers gain experience in this form of modeling, choosing algorithms, techniques, and frameworks that improve the quality, confidence level, and speed of development of their models. This increasing collective experience of complex systems modellers is a resource that should be captured. Fields such as software engineering and architecture have benefited from the development of generic solutions to recurring problems, called patterns. Using pattern development techniques from these fields, insights from communities such as learning and information processing, data mining, bioinformatics, and agent-based modeling can be identified and captured. Collections of such 'pattern languages' would allow knowledge gained through experience to be readily accessible to less-experienced practitioners and to other domains. This paper proposes a methodology for capturing the wisdom of computational modelers by introducing example visualization patterns, and a pattern classification system for analyzing the relationship between micro and macro behaviour in complex systems models. We anticipate that a new field of complex systems patterns will provide an invaluable resource for both practicing and future generations of modelers.

Vertical handover based adaptions for multimedia applications in pervasive systems

This paper proposes an architecture for pervasive computing which utilizes context information to provide adaptations based on vertical handovers (handovers between heterogeneous networks) while supporting application Quality of Service (QoS). The future of mobile computing will see an increase in ubiquitous network connectivity which allows users to roam freely between heterogeneous networks. One of the requirements for pervasive computing is to adapt computing applications or their environment if current applications can no longer be provided with the requested QoS. One of possible adaptations is a vertical handover to a different network. Vertical handover operations include changing network interfaces on a single device or changes between different devices. Such handovers should be performed with minimal user distraction and minimal violation of communication QoS for user applications. The solution utilises context information regarding user devices, user location, application requirements, and network environment. The paper shows how vertical handover adaptations are incorporated into the whole infrastructure of a pervasive system

Methods for conflict resolution in policy-based management systems

While developments in distributed object computing environments, such as the Common Object Request Broker Architecture (CORBA) [17] and the Telecommunication Intelligent Network Architecture (TINA) [16], have enabled interoperability between domains in large open distributed systems, managing the resources within such systems has become an increasingly complex task. This challenge has been considered for several years within the distributed systems management research community and policy-based management has recently emerged as a promising solution. Large evolving enterprises present a significant challenge for policy-based management partly due to the requirement to support both mutual transparency and individual autonomy between domains [2], but also because the fluidity and complexity of interactions occurring within such environments requires an ability to cope with the coexistence of multiple, potentially inconsistent policies. This paper discusses the need of providing both dynamic (run-time) and static (compile-time) conflict detection and resolution for policies in such systems and builds on our earlier conflict detection work [7, 8] to introduce the methods for conflict resolution in large open distributed systems.