Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Review of vibration-based damage detection and condition assessment of bridge structures using structural health monitoring

As a part of vital infrastructure and transportation networks, bridge structures must function safely at all times. However, due to heavier and faster moving vehicular loads and function adjustment, such as Busway accommodation, many bridges are now operating at an overload beyond their design capacity. Additionally, the huge renovation and replacement costs always make the infrastructure owners difficult to undertake. Structural health monitoring (SHM) is set to assess condition and foresee probable failures of designated bridge(s), so as to monitor the structural health of the bridges. The SHM systems proposed recently are incorporated with Vibration-Based Damage Detection (VBDD) techniques, Statistical Methods and Signal processing techniques and have been regarded as efficient and economical ways to solve the problem. The recent development in damage detection and condition assessment techniques based on VBDD and statistical methods are reviewed. The VBDD methods based on changes in natural frequencies, curvature/strain modes, modal strain energy (MSE) dynamic flexibility, artificial neural networks (ANN) before and after damage and other signal processing methods like Wavelet techniques and empirical mode decomposition (EMD) / Hilbert spectrum methods are discussed here.

Sustainable subdivisions – ventilation monitoring

Australia’s current pattern of residential development is typified by relatively low-density subdivision of land and highlights the necessity for development to be more sustainable to avoid unnecessary demand on natural resources and to prevent environmental degradation and to safeguard the environment for future generations. What role can climatically appropriate sub-division design play in decreasing the use of energy required to cool premises by maximising access to natural ventilation? How can this design be achieved?

Listening to nature : techniques for large-scale monitoring of ecosystems using acoustics

Climate change and human activity are subjecting the environment to unprecedented rates of change. Monitoring these changes is an immense task that demands new levels of automated monitoring and analysis. We propose the use of acoustics as a proxy for the time consuming auditing of fauna, especially for determining the presence/absence of species. Acoustic monitoring is deceptively simple; seemingly all that is required is a sound recorder. However there are many major challenges if acoustics are to be used for large scale monitoring of ecosystems. Key issues are scalability and automation. This paper discusses our approach to this important research problem. Our work is being undertaken in collaboration with ecologists interested both in identifying particular species and in general ecosystem health.

Listening to nature : acoustic monitoring of the environment

The requirement to monitor the rapid pace of environmental change due to global warming and to human development is producing large volumes of data but placing much stress on the capacity of ecologists to store, analyse and visualise that data. To date, much of the data has been provided by low level sensors monitoring soil moisture, dissolved nutrients, light intensity, gas composition and the like. However, a significant part of an ecologist’s work is to obtain information about species diversity, distributions and relationships. This task typically requires the physical presence of an ecologist in the field, listening and watching for species of interest. It is an extremely difficult task to automate because of the higher order difficulties in bandwidth, data management and intelligent analysis if one wishes to emulate the highly trained eyes and ears of an ecologist. This paper is concerned with just one part of the bigger challenge of environmental monitoring – the acquisition and analysis of acoustic recordings of the environment. Our intention is to provide helpful tools to ecologists – tools that apply information technologies and computational technologies to all aspects of the acoustic environment. The on-line system which we are building in conjunction with ecologists offers an integrated approach to recording, data management and analysis. The ecologists we work with have different requirements and therefore we have adopted the toolbox approach, that is, we offer a number of different web services that can be concatenated according to need. In particular, one group of ecologists is concerned with identifying the presence or absence of species and their distributions in time and space. Another group, motivated by legislative requirements for measuring habitat condition, are interested in summary indices of environmental health. In both case, the key issues are scalability and automation.

Monitoring the Australian Blogosphere through the 2007 Australian Federal Election

This paper examines the observable patterns of content creation by Australian political bloggers dur‐ing the 2007 election and its aftermath, thereby providing insight into the level and nature of activity in the Australian political blogosphere during that time. The performance indicators which are identi‐fied through this process enable us to target for further in‐depth research, to be reported in subse‐quent papers, those individual blogs and blog clusters showing especially high or unusual activity as compared to the overall baseline. This research forms the first stage in a larger project to investigate the shape and internal dynamics of the Australian political blogosphere. In this first stage, we tracked the activities of some 230 political blogs and related Websites in Australia from 2 November 2007 (the final month of the federal election campaign, with the election itself taking place on 24 Novem‐ber) to 24 January 2008. We harvested more than 65,000 articles for this study.

The big brother : monitoring urban growth and change for sustainable infrastructure provision

Monitoring urban growth and land-use change is an important issue for sustainable infrastructure planning. Rapid urban development, sprawl and increasing population pressure, particularly in developing nations, are resulting in deterioration of infrastructure facilities, loss of productive agricultural lands and open spaces, pollution, health hazards and micro-climatic changes. In addressing these issues effectively, it is crucial to collect up-to-date and accurate data and monitor the changing environment at regular intervals. This chapter discusses the role of geospatial technologies for mapping and monitoring the changing environment and urban structure, where such technologies are highly useful for sustainable infrastructure planning and provision.

Woodturning for older learners : a real 'turn on'

The research reported in this study concerns older adults from Australia who voluntarily chose to learn the craft of woodturning. Semi-structured interviews and a survey questionnaire were distributed to members of a woodturning club to explore their motivations and the processes by which they learned how to woodturn. The findings indicated that participants’ motivation could be construed as both intrinsic and extrinsic. They used seven approaches to learning – structured courses, instruction from convenors, modelling/watching/demonstrations, guided practice and monitoring by convenors, trial and error with practice, advice and help from peers and reading. Finally, the positive climate of the organisation was found to be particularly important to the older learners.

Source location of acoustic emission waves for structural health monitoring of bridges

The process of structural health monitoring (SHM) involves monitoring a structure over a period of time using appropriate sensors, extracting damage sensitive features from the measurements made by the sensors and analysing these features to determine the current state of the structure. Various techniques are available for structural health monitoring of structures and acoustic emission (AE) is one technique that is finding an increasing use. Acoustic emission waves are the stress waves generated by the mechanical deformation of materials. AE waves produced inside a structure can be recorded by means of sensors attached on the surface. Analysis of these recorded signals can locate and assess the extent of damage. This paper describes preliminary studies on the application of AE technique for health monitoring of bridge structures. Crack initiation or structural damage will result in wave propagation in solid and this can take place in various forms. Propagation of these waves is likely to be affected by the dimensions, surface properties and shape of the specimen. This, in turn, will affect source localization. Various laboratory test results will be presented on source localization, using pencil lead break tests. The results from the tests can be expected to aid in enhancement of knowledge of acoustic emission process and development of effective bridge structure diagnostics system.