Data analysis with artificial immune systems, cluster analysis and kohonen networks: some comparisons.

Neal M J Timmis J and Hunt J. Data analysis with artificial immune systems, cluster analysis and kohonen networks: some comparisons. In Proceedings of IEEE international conference of systems, man and cybernetics, pages 922-927, Tokyo, 1999. IEEE.

An artificial immune system for data analysis

Timmis J and Neal M J. An artificial immune system for data analysis. In Proceedings of 3rd international workshop on information processing in cells and tissues (IPCAT), Indianapolis, U.S.A., 1999.

A resource limited artificial immune system for data analysis.

Timmis J and Neal M J. A resource limited artificial immune system for data analysis. In Proceedings of ES2000 - Research and Development of Intelligent Systems, pages 19-32, Cambrige, U.K., 2000. Springer.

Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes

The ability to adapt to and respond to increases in external osmolarity is an important characteristic that enables bacteria to survive and proliferate in different environmental niches. When challenged with increased osmolarity, due to sodium chloride (NaCl) for example, bacteria elicit a phased response; firstly via uptake of potassium (K+), which is known as the primary response. This primary response is followed by the secondary response which is characterised by the synthesis or uptake of compatible solutes (osmoprotectants). The overall osmotic stress response is much broader however, involving many diverse cellular systems and processes. These ancillary mechanisms are arguably more interesting and give a more complete view of the osmotic stress response. The aim of this thesis was to identify novel genetic loci from the human gut microbiota that confer increased tolerance to osmotic stress using a functional metagenomic approach. Functional metagenomics is a powerful tool that enables the identification of novel genes from as yet uncultured bacteria from diverse environments through cloning, heterologous expression and phenotypic identification of a desired trait. Functional metagenomics does not rely on any previous sequence information to known genes and can therefore enable the discovery of completely novel genes and assign functions to new or known genes. Using a functional metagenomic approach, we have assigned a novel function to previously annotated genes; murB, mazG and galE, as well as a putative brp/blh family beta-carotene 15,15’-monooxygenase. Finally, we report the identification of a completely novel salt tolerance determinant with no current known homologues in the databases. Overall the genes identified originate from diverse taxonomic and phylogenetic groups commonly found in the human gastrointestinal (GI) tract, such as Collinsella and Eggerthella, Akkermansia and Bacteroides from the phyla Actinobacteria, Verrucomicrobia and Bacteroidetes, respectively. In addition, a number of the genes appear to have been acquired via lateral gene transfer and/or encoded on a prophage. To our knowledge, this thesis represents the first investigation to identify novel genes from the human gut microbiota involved in the bacterial osmotic stress response.

Examining Relationships between Culture, Creativity and Business Stage in an Emerging Market: A Categorical Data Analysis of Vietnam’s Data Set

In this article, we offer a new way of exploring relationships between three different dimensions of a business operation, namely the stage of business development, the methods of creativity and the major cultural values. Although separately, each of these has gained enormous attention from the management research community, evidenced by a large volume of research studies, there have been not many studies that attempt to describe the logic that connect these three important aspects of a business; let alone empirical evidences that support any significant relationships among these variables. The paper also provides a data set and an empirical investigation on that data set, using a categorical data analysis, to conclude that examinations of these possible relationships are meaningful and possible for seemingly unquantifiable information. The results also show that the most significant category among all creativity methods employed in Vietnamese enterprises is the “creative disciplines” rule in the “entrepreneurial phase,” while in general creative disciplines have played a critical role in explaining the structure of our data sample, for both stages of development in our consideration.

Qualitative analysis of the interdisciplinary interaction between data analysis specialists and novice clinical researchers.

BACKGROUND: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. METHODS/PRINCIPAL FINDINGS: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of "what if" situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. CONCLUSION/SIGNIFICANCE: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

[Book review] Chance encounters: a first course in data analysis and inference

Book review of: Chance Encounters: A First Course in Data Analysis and Inference by Christopher J. Wild and George A.F. Seber 2000, John Wiley & Sons Inc. Hard-bound, xviii + 612 pp ISBN 0-471-32936-3

A three-position spectral line survey of sagittarius B2 between 218 and 263 GHz. II. Data analysis

We present an analysis of the data from our Swedish-ESO Submillimetre Telescope molecular line survey in the 1.3 mm band of the N, M, and NW positions in the Sgr B2 molecular cloud. The line emissions from 42 molecular species, and some of their isotopomers, were analyzed assuming a single temperature and a homogeneous source. In cases where a source size much smaller than the antenna beam (23