Effect of pooling samples on the efficiency of comparative studies using microarrays

Motivation: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large.

Comparative analysis of synovial fluid and plasma proteomes in juvenile arthritis - Proteomic patterns of joint inflammation in early stage disease

Synovial fluid is a potential source of novel biomarkers for many arthritic disorders involving joint inflammation, including juvenile idiopathic arthritis. We first compared the distinctive protein ‘fingerprints’ of local inflammation in synovial fluid with systemic profiles within matched plasma samples. The synovial fluid proteome at the time of joint inflammation was then evaluated across clinical subgroups to identify early disease associated proteins. We measured the synovial fluid and plasma proteomes using the two-dimensional fluorescence difference gel electrophoresis approach. Image analysis software was used to highlight the expression levels of joint and subgroup associated proteins across the study cohort (n = 32). A defined subset of 30 proteins had statistically significant differences (p < 0.05) between sample types such that synovial fluid could be differentiated from plasma. Furthermore distinctive synovial proteome expression patterns segregate patient subgroups. Protein expression patterns localized in the chronically inflamed joint therefore have the potential to identify patients more likely to suffer disease which will spread from a single joint to multiple joints. The proteins identified could act as criteria to prevent disease extension by more aggressive therapeutic intervention directed at an earlier stage than is currently possible.

How could Human Rights Law be used by the Courts to assist Victims of Domestic Violence? A Comparative Study

It has been increasingly recognised in recent years that domestic violence constitutes a human rights issue. This article seeks to shed light on the question of how human rights law may be used in the area of domestic violence through the medium of a litigation strategy. The method used is a comparative assessment of the approaches taken towards gender issues by the Constitutional Courts in three states that have famously dynamic judiciaries- India, South Africa and Canada. A number of the obstacles to the effectiveness of human rights law are also examined.

The chronic fatigue syndrome: A comparative pathway analysis

In this paper, we introduce a method to detect pathological pathways of a disease. We aim to identify biological processes rather than single genes affected by the chronic fatigue syndrome (CFS). So far, CFS has neither diagnostic clinical signals nor abnormalities that could be diagnosed by laboratory examinations. It is also unclear if the CFS represents one disease or can be subdivided in different categories. We use information from clinical trials, the gene ontology (GO) database as well as gene expression data to identify undirected dependency graphs (UDGs) representing biological processes according to the GO database. The structural comparison of UDGs of sick versus non-sick patients allows us to make predictions about the modification of pathways due to pathogenesis.

Sexual size dimorphism and reproductive investment by female spiders: A comparative analysis

We investigate the association between female reproductive investment, absolute size, and sexual size dimorphism in spiders to test the predictions of the fecundity-advantage hypothesis. The relationships between absolute size and sexual size dimorphism and aspects of female reproductive output are examined in comparative analyses using phylogenetically independent contrasts. We provide support for the idea that allometry for sexual dimorphism is the result of variation in female size more so than male size. Regression analyses suggest selection for increased fecundity in females. We argue that fecundity selection provides the only general explanation for the evolution of sexual size dimorphism in spiders.