Methods Archive 

Abstract: Objectives: Microarray analysis requires standardized specimens and evaluation procedures to achieve acceptable results. A major limitation of this method is caused by heterogeneity in the cellular composition of tissue specimens, which frequently confounds data analysis. We introduce a linear model to deconfound gene expression data from tissue heterogeneity for genes exclusively expressed by a single cell type. Methods: Gene expression data are deconfounded from tissue heterogeneity effects by analyzing them using an appropriate linear regression model. In our illustrating data set tissue heterogeneity is being measured using flow cytometry. Gene expression data are determined in parallel by real time quantitative polymerase chain reaction (qPCR) and microarray analyses. Verification of deconfounding is enabled using protein quantification for the respective marker genes. Results: For our illustrating dataset, quantification of cell type proportions for peripheral blood mononuclear cells (PBMC) from tuberculosis patients and controls revealed differences in B cell and monocyte proportions between both study groups, and thus heterogeneity for the tissue under investigation. Gene expression analyses reflected these differences in celltype distribution. Fitting an appropriate linear model allowed us to deconfound measured transcriptome levels from tissue heterogeneity effects. In the case of monocytes, additional differential expression on the single cell level could be proposed. Protein quantification verified these deconfounded results. Conclusions: Deconfounding of transcriptome analyses for cellular heterogeneity greatly improves interpretability, and hence the validity of transcriptome profiling results.

Abstract: In May 1989, the International Symposium Medical Informatics and Education took place in Victoria B. C., Canada. It was the third conference organized under the auspices of the Working Group 1 "Education" of the International Medical Informatics Association (!MiA WG 1). It was at the same time the first symposium on this subject organized as an open conference on the basis of a general call for papers.

Abstract: Objectives: The International Medical Informatics Association (IMIA) today is an inclusive organization that represents the medical and health informatics world through its multiple member countries as well as affiliate, corporate and academic institutions, plus working groups and regions. The IMIA leadership deemed this is an excellent time to create a strategic alignment of IMIA’s goals and in turn to create a framework of the IMIA agenda for the future. Methods: The process began in early 2004, with a survey distributed to all IMIA members seeking members‘ views. The initial views were presented to the IMIA Board and General Assembly at Medinfo 2004 in San Francisco, USA. A Strategic Planning Task Force was established to take forward the development of a Strategic Plan. Through a combination of e-mail exchanges, face-to-face planning-discussion sessions in Geneva, Switzerland, and Washington DC, USA, and use of mediated conference calls, the IMIA Strategic Plan was evolved. Results: The framework model (also known as the IMIA rainbow umbrella) seeks to represent, in visual and descriptive terms, the numerous possibilities for connections and integration. Knowledge is the central core of IMIA. All of our strategies, interactions and efforts, emanate from this knowledge core. Using a concentric circle model, the next circle (from the central core) represents science. This is followed by the application layer circle, then the impact layer/circle and finally the outermost circle represents the people layer. Another dimensionality of the IMIA Strategic Plan is the need to represent various key sectors. There are six sectors superimposed on the five concentric circle layers of IMIA’s integration and connection to others. These sectors represent: health (our vision), research and science, behavioral responsibility, education, relationships and reach. Conclusion: We are still at a relatively early stage of planning. The Strategic Framework and Plan will be discussed by the IMIA Board and the IMIA General Assembly meeting (November 2006).

Abstract: Clinical algorithms for cancer chemotherapy--systems for community-based consultant-extenders and oncology centers. -