Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Are free condoms associated with the frequent use of condoms among men who have sex with men?

Introduction. The National Behavioral HIV Surveillance (NHBS) is a self-reported cross-sectional survey that monitors the spread of human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). The 2004 survey asked if the participant received a free condom, used it, and if receiving a free condom made him more likely to use a condom. The aim of this cross-sectional study is to examine the Houston MSA sub-dataset to determine if there was a self-expressed association between receiving a free condom and likelihood of using a condom at next intercourse, and to determine if the strength of that association varied by demographic subgroup.^ Methods. The Houston MSA 2004 NHBS had 502 participants who were men who have sex with men (MSM). The present analysis examined the answers to the questions: "In the past 12 months, have you received free condoms?" "Have you used any of the free condoms you received?" and "Did getting these free condoms make you more likely to use condoms during sex?".^ Results. Out of 502 participants, 500 answered the question about receiving free condoms, 406 (81.2%) answered all three questions, and 204 (50.2%) answered "yes" to all three questions. In the subgroup analyses, Hispanics were significantly less likely and men under 29 years of age were significantly more likely to report that their condom use behavior was influenced by receiving a free condom. ^ Conclusion. The effect of receipt of free condoms on likelihood of condom use varies by demographic subgroup, but these potentially important preliminary findings will require further investigation to validate them and further explicate the possible underlying dynamics.^