Temporal relationship between the auditory brainstem response and focal responses of auditory nerve root and cochlear nucleus during development in the tammar wallaby (Macropus eugenii)

Thirty-two pouch-young tammar wallabies were used to discover the generators of the auditory brainstem response (ABR) during development by the use of simultaneous ABR and focal brainstem recordings. A click response from the auditory nerve root (ANR) in the wallaby was recorded from postnatal day (PND) 101, when no central auditory station was functional, and coincided with the ABR, a simple positive wave. The response of the cochlear nucleus (CN) was detected from PND 110, when the ABR had developed 1 positive and 1 negative peak. The dominant component of the focal ANR response, the N-1 wave, coincided with the first half of the ABR P wave, and that of the focal CN response, the N-1 wave, coincided with the later two thirds. In older animals, the ANR response coincided with the ABR's N-1, wave, while the CN response coincided with the ABR's P-2, N-2 and P-3 waves, with its contribution to the ABR P-2 dominant. The protracted development of the marsupial auditory system which facilitated these correlations makes the tammar wallaby a particularly suitable model. Copyright (C) 2001 S. Karger AG, Basel.

SubCM: A tool for improved visibility of software change in an industrial setting

Software Configuration Management is the discipline of managing large collections of software development artefacts from which software products are built. Software configuration management tools typically deal with artefacts at fine levels of granularity - such as individual source code files - and assist with coordination of changes to such artefacts. This paper describes a lightweight tool, designed to be used on top of a traditional file-based configuration management system. The add-on tool support enables users to flexibly define new hierarchical views of product structure, independent of the underlying artefact-repository structure. The tool extracts configuration and change data with respect to the user-defined hierarchy, leading to improved visibility of how individual subsystems have changed. The approach yields a range of new capabilities for build managers, and verification and validation teams. The paper includes a description of our experience using the tool in an organization that builds large embedded software systems.

Procedure compilation in the refinement calculus

High-level language program compilation strategies can be proven correct by modelling the process as a series of refinement steps from source code to a machine-level description. We show how this can be done for programs containing recursively-defined procedures in the well-established predicate transformer semantics for refinement. To do so the formalism is extended with an abstraction of the way stack frames are created at run time for procedure parameters and variables.

Type X pottery, Morobe Province, Papua New Guinea: Petrography and possible Micronesian relationships

Type X is one of four Post-Lapita pottery styles reported from Huon Peninsula and the Siassi Islands of Papua New Guinea. Previous petrographic work was inconclusive about its likely area of origin but indicated a possible Huon Peninsula source. Renewed analysis of a larger sample supports this conclusion and confirms the use of grog temper. This kind of temper is otherwise not recorded in the New Guinea region, and its use in the production of Type X was probably culturally driven. Comparisons between Type X and grog-tempered pottery from Palau, Yap, and Pohnpei in Micronesia lead to the suggestion that Type X probably derived from an otherwise unrecorded contact between Huon Peninsula and Palau about 1000 years ago. The article reviews other evidence for interaction between the New Guinea-Bismarck Archipelago region and various parts of Micronesia and concludes that the proposed Type X connection with Palau is but one of several prehistoric contacts between different parts of the regions. Recognition of such contacts, which could have been unintentional and on a small scale, may contribute to explaining the complex ethnolinguistic situation of Huon Peninsula.

Maximising the information gained from an experimental analysis of code inspection and static analysis for concurrent Java components

The results of empirical studies are limited to particular contexts, difficult to generalise and the studies themselves are expensive to perform. Despite these problems, empirical studies in software engineering can be made effective and they are important to both researchers and practitioners. The key to their effectiveness lies in the maximisation of the information that can be gained by examining existing studies, conducting power analyses for an accurate minimum sample size and benefiting from previous studies through replication. This approach was applied in a controlled experiment examining the combination of automated static analysis tools and code inspection in the context of verification and validation (V&V) of concurrent Java components. The combination of these V&V technologies was shown to be cost-effective despite the size of the study, which thus contributes to research in V&V technology evaluation.

Timing analysis of assembler code control-flow paths

Timinganalysis of assembler code is essential to achieve the strongest possible guarantee of correctness for safety-critical, real-time software. Previous work has shown how timingconstrain ts on controlflow paths through high-level language programs can be formalised using the semantics of the statements comprisingthe path. We extend these results to assembler-level code where it becomes possible to not only determine timingconstrain ts, but also to verify them against the known execution times for each instruction. A minimal formal model is developed with both a weakest liberal precondition and a strongest postcondition semantics. However, despite the formalism’s simplicity, it is shown that complex timingb ehaviour associated with instruction pipeliningand iterative code can be modelled accurately.

A state-contingent production approach to principal-agent problems with an application to point-source pollution control

Two basic representations of principal-agent relationships, the 'state-space' and 'parameterized distribution' formulations, have emerged. Although the state-space formulation appears more natural, analytical studies using this formulation have had limited success. This paper develops a state-space formulation of the moral-hazard problem using a general representation of production under uncertainty. A closed-form solution for the agency-cost problem is derived. Comparative-static results are deduced. Next we solve the principal's problem of selecting the optimal output given the agency-cost function. The analysis is applied to the problem of point-source pollution control. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Quantitative analysis of the time courses of enzyme-catalyzed reactions

The catalytic properties of enzymes are usually evaluated by measuring and analyzing reaction rates. However, analyzing the complete time course can be advantageous because it contains additional information about the properties of the enzyme. Moreover, for systems that are not at steady state, the analysis of time courses is the preferred method. One of the major barriers to the wide application of time courses is that it may be computationally more difficult to extract information from these experiments. Here the basic approach to analyzing time courses is described, together with some examples of the essential computer code to implement these analyses. A general method that can be applied to both steady state and non-steady-state systems is recommended. (C) 2001 academic Press.

Evidence for the presence of a widespread PCDD source in coastal sediments and soils from Queensland, Australia

Recent studies have demonstrated the occurrence of elevated levels of higher chlorinated PCDDs in the coastal environment of Queensland, Australia. This study presents new data for OCDD contamination and full PCDD/F profile analysis in the environment of Queensland. Marine sediments, irrigation drain sediments and topsoil were collected from sites that were expected to be influenced by specific land-use types. High OCDD concentrations were associated mainly with sediments collected near the mouth of rivers which drain into large catchments in the tropical and subtropical regions. Further, analysis of sediments from irrigation drains could be clearly differentiated on the basis of OCDD contamination, with high concentrations in samples from sugarcane drains collected from coastal regions, and low concentrations in drain sediments from drier inland cotton growing areas. PCDD/F congener-specific analysis demonstrated almost identical congener profiles in all samples collected along the coastline. This indicates the source to be widespread. Profiles were dominated by higher chlorinated PCDDs, in particular OCDD whereas 2,3,7,8-substituted PCDFs were below the limit of quantification in the majority of samples. The full PCDD/F profile analysis of samples strongly resemble those reported for lake sediments from Mississippi and kaolinite samples from Germany, Strong similarities to these samples with respect to congener profiles and isomer patterns may indicate the presence of a similar source and/or formation process that is yet unidentified. (C) 2001 Elsevier Science Ltd. All rights reserved.

Development of a novel titration and off-gas analysis (TOGA) sensor for study of biological processes in wastewater treatment systems

The development of the new TOGA (titration and off-gas analysis) sensor for the detailed study of biological processes in wastewater treatment systems is outlined. The main innovation of the sensor is the amalgamation of titrimetric and off-gas measurement techniques. The resulting measured signals are: hydrogen ion production rate (HPR), oxygen transfer rate (OTR), nitrogen transfer rate (NTR), and carbon dioxide transfer rate (CTR). While OTR and NTR are applicable to aerobic and anoxic conditions, respectively, HPR and CTR are useful signals under all of the conditions found in biological wastewater treatment systems, namely, aerobic, anoxic and anaerobic. The sensor is therefore a powerful tool for studying the key biological processes under all these conditions. A major benefit from the integration of the titrimetric and off-gas analysis methods is that the acid/base buffering systems, in particular the bicarbonate system, are properly accounted for. Experimental data resulting from the TOGA sensor in aerobic, anoxic, and anaerobic conditions demonstrates the strength of the new sensor. In the aerobic environment, carbon oxidation (using acetate as an example carbon source) and nitrification are studied. Both the carbon and ammonia removal rates measured by the sensor compare very well with those obtained from off-line chemical analysis. Further, the aerobic acetate removal process is examined at a fundamental level using the metabolic pathway and stoichiometry established in the literature, whereby the rate of formation of storage products is identified. Under anoxic conditions, the denitrification process is monitored and, again, the measured rate of nitrogen gas transfer (NTR) matches well with the removal of the oxidised nitrogen compounds (measured chemically). In the anaerobic environment, the enhanced biological phosphorus process was investigated. In this case, the measured sensor signals (HPR and CTR) resulting from acetate uptake were used to determine the ratio of the rates of carbon dioxide production by competing groups of microorganisms, which consequently is a measure of the activity of these organisms. The sensor involves the use of expensive equipment such as a mass spectrometer and requires special gases to operate, thus incurring significant capital and operational costs. This makes the sensor more an advanced laboratory tool than an on-line sensor. (C) 2003 Wiley Periodicals, Inc.

Testing insect movement theory: empirical analysis of pest data routinely collected from agricultural crops

Observations of an insect's movement lead to theory on the insect's flight behaviour and the role of movement in the species' population dynamics. This theory leads to predictions of the way the population changes in time under different conditions. If a hypothesis on movement predicts a specific change in the population, then the hypothesis can be tested against observations of population change. Routine pest monitoring of agricultural crops provides a convenient source of data for studying movement into a region and among fields within a region. Examples of the use of statistical and computational methods for testing hypotheses with such data are presented. The types of questions that can be addressed with these methods and the limitations of pest monitoring data when used for this purpose are discussed. (C) 2002 Elsevier Science B.V. All rights reserved.

Monitoring the composition and form of urban environments based on the vegetation-impervious surface-soil (VIS) model by sub-pixel analysis techniques

The majority of the world's population now resides in urban environments and information on the internal composition and dynamics of these environments is essential to enable preservation of certain standards of living. Remotely sensed data, especially the global coverage of moderate spatial resolution satellites such as Landsat, Indian Resource Satellite and Systeme Pour I'Observation de la Terre (SPOT), offer a highly useful data source for mapping the composition of these cities and examining their changes over time. The utility and range of applications for remotely sensed data in urban environments could be improved with a more appropriate conceptual model relating urban environments to the sampling resolutions of imaging sensors and processing routines. Hence, the aim of this work was to take the Vegetation-Impervious surface-Soil (VIS) model of urban composition and match it with the most appropriate image processing methodology to deliver information on VIS composition for urban environments. Several approaches were evaluated for mapping the urban composition of Brisbane city (south-cast Queensland, Australia) using Landsat 5 Thematic Mapper data and 1:5000 aerial photographs. The methods evaluated were: image classification; interpretation of aerial photographs; and constrained linear mixture analysis. Over 900 reference sample points on four transects were extracted from the aerial photographs and used as a basis to check output of the classification and mixture analysis. Distinctive zonations of VIS related to urban composition were found in the per-pixel classification and aggregated air-photo interpretation; however, significant spectral confusion also resulted between classes. In contrast, the VIS fraction images produced from the mixture analysis enabled distinctive densities of commercial, industrial and residential zones within the city to be clearly defined, based on their relative amount of vegetation cover. The soil fraction image served as an index for areas being (re)developed. The logical match of a low (L)-resolution, spectral mixture analysis approach with the moderate spatial resolution image data, ensured the processing model matched the spectrally heterogeneous nature of the urban environments at the scale of Landsat Thematic Mapper data.

Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

Mouse proteome analysis

A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteornes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins