Analyzing inconsistency toward enhancing integration of biological molecular databases

The rapid growth of biological databases not only provides biologists with abundant data but also presents a big challenge in relation to the analysis of data. Many data analysis approaches such as data mining, information retrieval and machine learning have been used to extract frequent patterns from diverse biological databases. However, the discrepancies, due to the differences in the structure of databases and their terminologies, result in a significant lack of interoperability. Although ontology-based approaches have been used to integrate biological databases, the inconsistent analysis of biological databases has been greatly disregarded. This paper presents a method by which to measure the degree of inconsistency between biological databases. It not only presents a guideline for correct and efficient database integration, but also exposes high quality data for data mining and knowledge discovery.

Chronic mental stress is a cause of essential hypertension : presence of biological markers of stress

1. In searching for biological evidence that essential hypertension is caused by chronic mental stress, a disputed proposition, parallels are noted with panic disorder, which provides an explicit clinical model of recurring stress responses.
2. There is clinical comorbidity; panic disorder prevalence is increased threefold in essential hypertension. Plasma cortisol is elevated in both.
3. In panic disorder and essential hypertension, but not in health, single sympathetic nerve fibres commonly fire repeatedly within an individual cardiac cycle; this appears to be a signature of stress exposure. For both conditions, adrenaline cotransmission is present in sympathetic nerves.
4. Tissue nerve growth factor is increased in both (nerve growth factor is a stress reactant). There is induction of the adrenaline synthesizing enzyme, phenylethanolamine-N-methyltransferase, in sympathetic nerves, an explicit indicator of mental stress exposure.
5. The question of whether chronic mental stress causes high blood pressure, still hotly debated, has been reviewed by an Australian Government body, the Specialist Medical Review Council. Despite the challenging medicolegal implications, the Council determined that stress is one proven cause of hypertension, this ruling being published in the 27 March 2002 Australian Government Gazette. This judgement was reached after consideration of the epidemiological evidence, but in particular after review of the specific elements of the neural pathophysiology of essential hypertension, described above.

The division of labor, capital, communication technology and economic growth : the case of China 1952–99

The implications of the division of labor, capital, and technology for economic growth have long been a fundamental issue in development economics. This paper employs the bounds testing approach to cointegration to examine the relationship between the division of labor, capital accumulation, communication technology, and economic growth for China over the period 1952–99. We find that in the long run, capital stock and the division of labor both have statistically significant positive effects on growth, while in the short run the effects are not significantly positive. Telecommunication technology, rather surprisingly, has a statistically insignificant impact on growth both in the long run and in the short run. Our findings indicate that there exists a long run equilibrium relationship between capital and the division of labor on the one hand, and economic growth on the other, thereby lending support to the division of labor theory of growth.

The development of biological objectives for streams in a single catchment: a case study on the catchment of western port bay, Victoria, Australia

Government environment protection policies for waterways have traditionally relied on water quality indicators and their objectives. In this paper we describe the development of biological objectives based on invertebrate indicators for inclusion in a government policy for the catchment of Western Port Bay, Victoria. The first step of defining segments (areas with streams in which the same objectives are applied) was problematic, requiring two different approaches, as follows. Site groups initially based on invertebrate community composition derived using multivariate techniques (ordination and classification) proved to be unsuitable for policy segments. Segment boundaries were subsequently defined using topographical (e.g. boundary of foothills and lowland plains), climate (e.g. rainfall) and land-use (e.g. urban) features. We used information and data from reference sites inside as well outside the catchment to derive specific biological objectives based on aquatic invertebrates for these segments. Objectives were specified for the following four indicators – number of invertebrate families, the SIGNAL index, the AUSRIVAS predictive model and the number of key families.

Development of monoclonal antibodies against Vibrio pathogens

Monoclonal antibodies were developed against pathogenic vibrios for use in rapid identification in disease situations of humans, fish and shellfish. Of the 12 fusions performed using V. alginolyticus, V. anguillarum, V. carchariae, V. cholerae, V. damsela, V. furnissii, V. harveyi, V. ordalii, V. parahaemolyticus and V. vulnificus, a total of 102 hybridomas were obtained. Based on cross-reactivity of a wide range of Vibrio strains and other gram-negative bacteria, three broad types of monoclonal antibodies were found. The three categories were: (1) ones that were species-specific or specific to a particular surface antigen, (2) a large number that reacted with several Vibrio species, and (3) three that reacted with most Vibrio strains but no other gram-negative bacteria. Each species-specific monoclonal antibody only recognized its corresponding Vibrio species and was used for identifying unknown species, confirming diagnosis of clinical isolates. In addition, several monoclonal antibodies only cross-reacted with similar Vibrio species, e.g. V. parahaemolyticus and V. alginolyticus which share a common H-antigen. Monoclonal antibodies reacting with several Vibrio species were not of particular use in diagnostic situations. Three monoclonal antibodies of the last group did not react with other genera of the family Vibrionaceae, namely Aeromonas, Photobacterium and Plesiomonas nor a wide range of gram-negative enteric bacteria. These data indicated the existence of an antigenic surface determinant common to Vibrio species. One monoclonal reacted with the heat-stable antigenic determinants on the cell surface as v as lipopolysaccharide extracted from all the vibrios studied, thus making it useful for large- scale screening of acute infections of vibrios. In a blind test, seven Vibrio species, isolated from 6 marine and a freshwater source were identified by two laboratories using phenetic tests. Results of immunotyping using monoclonals, three of seven were diagnosed as the same species, another three were designated as Vibrio species but could not be classified further due to the library not having the corresponding monoclonal, and one was diagnostically questionable. Two further tests were carried out. An unknown Vibrio formalin-fixed isolated from diseased marine animal was identified as V. parahaemolyticus by ELISA and FITC. Clinical human isolates of V. alginolyticus, V. parahaemolyticus and V. vulnificus were confirmed by monoclonals. Australian isolates of V. anguillarum appeared to be mostly of serotype O1. monoclonals raised to V. anguillarum AFHRL 1 reacted with only serotype O1 from Denmark but also most Australian isolates. All vibrios pathogenic to fish and shellfish, i.e. V. anguillarum, V. ordalii, V. alginolyticus, V. carchariae, V. cholerae, V. damsela, V. harveyi, V. parahaemolyticus and V. vulnificus, were used for attachment studies to fish cells using phase contrast and FITC-immunofluorescence microscopy. Of these vibrios, V. anguillarum, V. ordalii and V. perahaemolyticus, were found to adhere to different cells and tissues of rainbow trout while others did not appear to attach. However, attachment was inhibited by monoclonal antibodies specific to only these three vibrios. Lipopolysaccharide is well known as being a contributing factor in pathogenicity of gram-negative bacteria. PAGE electrophoresis of extracted LPS from 9 strains covering 6 Vibrio species showed the presence of a common 15,000 D fragment. This fragment was verified by immunoblotting with a genus-specific monoclonal antibody (i.e. F11P411F) recognizing nearly all vibrios. The common LPS fragment was separated and used to raise polyclonal antisera in mouse which reacted strongly with LPS itself, live as well as sodium azide-killed vibrios, but not with other gram-negative bacteria. This raised the possibility of developing vaccine from Vibrio LPS. Monoclonal antibodies developed in the present study enabled rapid identification of a number of pathogenic Vibrio species. There is still further work to produce monoclonal antibodies against additional vibrios that are probably pathogenic. These included V. fluvialis, V. hollisae, V. metschnikovii, V. minicus, V. salmonella and V. tubiashii. Together the application will be of significance in clinical diagnostic work, in the monitoring of vibriosis in fish farms and in quarantine.

Developing a collections management policy for the Ethnology Division of the National Museum, Monuments and Art Gallery of Botswana

The culture and political environments of Botswana influence the collections management policy of its' National Museum, Monuments and Art Gallery. The emphasis of this research is to make the museum relevent to the needs of the local people by developing more suitable ideas. The developed policy is intended to reflect these unique needs.

Dual-random ensemble method for multi-label classification of biological data

This paper presents a dual-random ensemble multi-label classification method for classification of multi-label data. The method is formed by integrating and extending the concepts of feature subspace method and random k-label set ensemble multi-label classification method. Experiemental results show that the developed method outperforms the exisiting multi-lable classification methods on three different multi-lable datasets including the biological yeast and genbase datasets.