MHCWeb: Converting a WWW database into a knowledge-based collaborative environment

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary, We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The 0 WEB environment allows for flexible access to the data by both users and computer programs.

Practical considerations for the measurement of free light chains in serum

Background: A new immunoassay for free light chain measurements has been reported to be useful for the diagnosis and monitoring of monoclonal light chain diseases and nonsecretory myeloma. We describe experience with and some potential pitfalls of the assay. Methods: The assay was assessed for precision, sample type and stability, recovery, and harmonization of results between two analyzers on which the reagents are used. Free-light-chain concentrations were measured in healthy individuals (to determine biological variation), patients with monoclonal gammopathy of undetermined significance, myeloma patients after autologous stem cell transplants, and patients with renal disease. Results: Analytical imprecision (CV) was 6-11% for kappa and A free-light-chain measurement and 16% for the calculated kappa/lambda ratio. Biological variation was generally insignificant compared with analytical variation. Despite the same reagent source, values were not completely harmonized between assay systems and may produce discordant free-light-chain ratios. In some patients with clinically stable myeloma, or post transplantation, or with monoclonal gammopathy of undetermined significance, free-light-chain concentration and ratio were within the population reference interval despite the presence of monoclonal intact immunoglobulin in serum. In other patients with monoclonal gammopathy of undetermined significance, values were abnormal although there was no clinical evidence of progression to multiple myeloma. Conclusions: The use of free-light-chain measurements alone cannot differentiate some groups of patients with monoclonal gammopathy from healthy individuals. As with the introduction of any new test, it is essential that more scientific data about use of this assay in different subject groups are available so that results can be interpreted with clinical certainty. (C) 2003 American Association for Clinical Chemistry.

Accuracy of SRM and power tap power monitoring systems for bicycling

Purpose: Although manufacturers of bicycle power monitoring devices SRM and Power Tap (PT) claim accuracy to within 2.5%, there are limited scientific data available in support. The purpose of this investigation was to assess the accuracy of SRM and PT under different conditions. Methods: First, 19 SRM were calibrated, raced for 11 months, and retested using a dynamic CALRIG (50-1000 W at 100 rpm). Second, using the same procedure, five PT were repeat tested on alternate days. Third, the most accurate SRM and PT were tested for the influence of cadence (60, 80, 100, 120 rpm), temperature (8 and 21degreesC) and time (1 h at similar to300 W) on accuracy. Finally, the same SRM and PT were downloaded and compared after random cadence and gear surges using the CALRIG and on a training ride. Results: The mean error scores for SRM and PT factory calibration over a range of 50-1000 W were 2.3 +/- 4.9% and -2.5 +/- 0.5%, respectively. A second set of trials provided stable results for 15 calibrated SRM after 11 months (-0.8 +/- 1.7%), and follow-up testing of all PT units confirmed these findings (-2.7 +/- 0.1%). Accuracy for SRM and PT was not largely influenced by time and cadence; however. power output readings were noticeably influenced by temperature (5.2% for SRM and 8.4% for PT). During field trials, SRM average and max power were 4.8% and 7.3% lower, respectively, compared with PT. Conclusions: When operated according to manufacturers instructions, both SRM and PT offer the coach, athlete, and sport scientist the ability to accurately monitor power output in the lab and the field. Calibration procedures matching performance tests (duration, power, cadence, and temperature) are, however, advised as the error associated with each unit may vary.

Biological monitoring and Biological Limit Values (BLV): The strategy of the European Union

Occupational standards concerning allowable concentrations of chemical compounds in the ambient air of workplaces have been established in several countries worldwide. With the integration of the European Union (EU), there has been a need of establishing harmonised Occupational Exposure Limits (OEL). The European Commission Directive 95/320/EC of 12 July 1995 has given the tasks to a Scientific Committee for Occupational Exposure Limits (SCOEL) to propose, based on scientific data and where appropriate, occupational limit values which may include the 8-h time-weighted average (TWA), short-term limits/excursion limits (STEL) and Biological Limit Values (BLVs). In 2000, the European Union issued a list of 62 chemical substances with Occupational Exposure Limits. Of these, 25 substances received a skin notation, indicating that toxicologically significant amounts may be taken up via the skin. For such substances, monitoring of concentrations in ambient air may not be sufficient, and biological monitoring strategies appear of potential importance in the medical surveillance of exposed workers. Recent progress has been made with respect to formulation of a strategy related to health-based BLVs. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.