Tool support for executable documentation of Java class hierarchies

While object-oriented programming offers great solutions for today's software developers, this success has created difficult problems in class documentation and testing. In Java, two tools provide assistance: Javadoc allows class interface documentation to be embedded as code comments and JUnit supports unit testing by providing assert constructs and a test framework. This paper describes JUnitDoc, an integration of Javadoc and JUnit, which provides better support for class documentation and testing. With JUnitDoc, test cases are embedded in Javadoc comments and used as both examples for documentation and test cases for quality assurance. JUnitDoc extracts the test cases for use in HTML files serving as class documentation and in JUnit drivers for class testing. To address the difficult problem of testing inheritance hierarchies, JUnitDoc provides a novel solution in the form of a parallel test hierarchy. A small controlled experiment compares the readability of JUnitDoc documentation to formal documentation written in Object-Z. Copyright (c) 2005 John Wiley & Sons, Ltd.

Dominance hierarchies and health: Constructing personal zones of spiritual power and healing in modern medicine

Ethological studies of animals in groups and sociobiology indicate that hierarchies of dominance amongst some species ensure the survival of the group. When transferred to human groups, dominance hierarchies suggest a crucial role played by recasting the scope of such hierarchies of dominant and subordinate members to included hyper-dominant beings. A recognition of such beings as even more dominant than the socially dominant members of a hierarchy facilitates the empowerment of the socially subordinate members. Religious belief and practice works to establish such hyper-dominant beings (gods, goddesses, and so forth) as superior members of human groups. Doing so is a means of ensuring the survival of the species and, thus, enhancing healing and human health. The doctor-patient relationship is examined from such a point of view, with an emphasis on whether the hierarchy created by the relationship allows consideration of alternative and complementary forms of medical treatment.

The paradox of managerial downsizing

Delayering and the flattening of organizational hierarchies was a widespread trend through the 1990s. Peters (1992) in the USA promoted flattening as an organizational strategy and Keuning and Opheij (1994) promoted the prescriptions in Europe. Despite these strategies and apparent structural changes, the number and ratio of managers appears to have grown. This paradox of managerial downsizing has not been adequately probed in the literature. The predominant explanation, that there has been a 'myth of managerial downsizing', is associated with Gordon (1996). However, this debate has been shaped by the US experience and data. There is a need to reassess the dynamics of the 1990s in relation to other economies. This article focuses on a semi-peripheral economy, that of Australia. A study of the population of firms over time is necessary in order to resolve the issues. The article utilizes a comprehensive range of data, including several national surveys and a longitudinal database of all larger private-sector firms in Australia during the 1990s. The results indicate that the 'myth of managerial downsizing' must be rejected. There were dramatic effects on managers through the course of the 1990s in larger Australian firms. The dynamics of the process are analysed, tracking 4,153 firms across the decade and the paradox explained. The theoretical implications are discussed.

Male reproductive tactics and female choice in the solitary, promiscuous bridled nailtail wallaby (Onychogalea fraenata)

Several behavioral studies of large, gregarious, and sexually dimorphic macropods have shown that males form dominance hierarchies and large males have the highest reproductive success. The bridled nailtail wallaby (Onychogalea fraenata) is a smaller and strongly sexually dimorphic macropod, but is also highly solitary and males do not form dominance hierarchies that are maintained temporally or spatially. Genetic studies of paternity have shown that large males are the most reproductively successful and only one-quarter of males sire offspring at any one time. The aim of this study was to investigate the tactics that males adopt to secure access to females at the time of estrus and to investigate whether females can influence which males have access to them. This study was conducted using 2 wild, free-ranging populations of bridled nailtail wallabies. Females in estrus were located and observed. and the total number of males present, the relative weight rank of each mate, and interactions between individuals were recorded. Females showed a preference for large males and incited male-male competition when the group of males present was large. Unlike other dimorphic macropods, fights among males were rare and were restricted to males of similar size. Large males gained access to females by guarding and following them closely and threatening other males who attempted to gain access. Smaller males spent less time with females, suggesting that small males may leave multimale groups in an attempt to locate unguarded females. Given the solitary nature of this species and the lack of a stable dominance hierarchy to influence male reproductive success. mate searching and mate guarding may be important male reproductive tactics in this species.

Multilevel modelling for inference of genetic regulatory networks

Time-course experiments with microarrays are often used to study dynamic biological systems and genetic regulatory networks (GRNs) that model how genes influence each other in cell-level development of organisms. The inference for GRNs provides important insights into the fundamental biological processes such as growth and is useful in disease diagnosis and genomic drug design. Due to the experimental design, multilevel data hierarchies are often present in time-course gene expression data. Most existing methods, however, ignore the dependency of the expression measurements over time and the correlation among gene expression profiles. Such independence assumptions violate regulatory interactions and can result in overlooking certain important subject effects and lead to spurious inference for regulatory networks or mechanisms. In this paper, a multilevel mixed-effects model is adopted to incorporate data hierarchies in the analysis of time-course data, where temporal and subject effects are both assumed to be random. The method starts with the clustering of genes by fitting the mixture model within the multilevel random-effects model framework using the expectation-maximization (EM) algorithm. The network of regulatory interactions is then determined by searching for regulatory control elements (activators and inhibitors) shared by the clusters of co-expressed genes, based on a time-lagged correlation coefficients measurement. The method is applied to two real time-course datasets from the budding yeast (Saccharomyces cerevisiae) genome. It is shown that the proposed method provides clusters of cell-cycle regulated genes that are supported by existing gene function annotations, and hence enables inference on regulatory interactions for the genetic network.