Extracting and explaining biological knowledge in microarray data

© Springer-Verlag Berlin Heidelberg 2004. This paper describes a method of clustering lists of genes mined from a microarray dataset using functional information from the Gene Ontology. The method uses relationships between terms in the ontology both to build clusters and to extract meaningful cluster descriptions. The approach is general and may be applied to assist explanation of other datasets associated with ontologies

Comparing Cost-Effectiveness of HIV Testing Strategies: Targeted and Routine Testing in Washington, DC.

BACKGROUND: Routine HIV testing is an essential approach to identifying undiagnosed infections, linking people to care and treatment, and preventing new infections. In Washington, DC, where HIV prevalence is 2.4%, a combination of routine and targeted testing approaches has been implemented since 2006. METHODS: We sought to evaluate the cost effectiveness of the District of Columbia (DC) Department of Health\u27s routine and targeted HIV testing implementation strategies. We collected HIV testing data from 3 types of DC Department of Health-funded testing sites (clinics, hospitals, and community-based organizations); collected testing and labor costs; and calculated effectiveness measures including cost per new diagnosis and cost per averted transmission. RESULTS: Compared to routine testing, targeted testing resulted in higher positivity rates (1.33% vs. 0.44%). Routine testing averted 34.30 transmissions per year compared to targeted testing at 17.78. The cost per new diagnosis was lower for targeted testing ($2,467 vs.$7,753 per new diagnosis) as was the cost per transmission averted ($33,160 vs.$104,205). When stratified by testing site, both testing approaches were most cost effective in averting new transmissions when conducted by community based organizations ($25,037 routine;$33,123 targeted) compared to hospitals or clinics. CONCLUSIONS: While routine testing identified more newly diagnosed infections and averted more infections than targeted testing, targeted testing is more cost effective per diagnosis and per transmission averted overall. Given the high HIV prevalence in DC, the DC Department of Health\u27s implementation strategy should continue to encourage routine testing implementation with emphasis on a combined testing strategy among community-based organizations

HIV testing implementation in two urban cities: Practice, policy and perceived barriers

Background Although funding has supported the scale up of routine, opt-out HIV testing in the US, variance in implementation mechanisms and barriers in high-burden jurisdictions remains unknown. Methods We conducted a survey of health care organizations in Washington, DC and Houston/Harris County to determine number of HIV tests completed in 2011, policy and practices associated with HIV testing, funding mechanisms, and reported barriers to testing in each jurisdiction and to compare results between jurisdictions. Results In 2012, 43 Houston and 35 DC HIV-testing organizations participated in the survey. Participants represented 85% of Department of Health-supported testers in DC and 90% of Department of Health-supported testers in Houston. The median number of tests per organization was 568 in DC and 1045 in Houston. Approximately 50% of organizations in both DC and Houston exclusively used opt-in consent and most conducted both pre- and post-test counseling with HIV testing (80% of organizations in DC, 70% in Houston). While the most frequent source of funding in DC was the Department of Health, Houston organizations primarily billed the patient or third-party payers. Barriers to testing most often reported were lack of funding, followed by patient discomfort/refusal with more barriers reported in DC. Conclusions Given unique policies, resources and programmatic contexts, DC and Houston have taken different approaches to support routine testing. Many organizations in both cities reported opt-in consent approaches and pre-test counseling, suggesting 2006 national HIV testing recommendations are not being followed consistently. Addressing the barriers to testing identified in each jurisdiction may improve expansion of testing

Parallel computing in information retrieval - An updated review

The progress of parallel computing in Information Retrieval (IR) is reviewed. In particular we stress the importance of the motivation in using parallel computing for Text Retrieval. We analyse parallel IR systems using a classification due to Rasmussen [1] and describe some parallel IR systems. We give a description of the retrieval models used in parallel Information Processing.. We describe areas of research which we believe are needed

Limits on the effective quark radius from inclusive epep scattering at HERA

The high-precision HERA data allows searches up to TeV scales for Beyond the Standard Model contributions to electron-quark scattering. Combined measurements of the inclusive deep inelastic cross sections in neutral and charged current $ep$ scattering corresponding to a luminosity of around 1 fb$^{-1}$ have been used in this analysis. A new approach to the beyond the Standard Model analysis of the inclusive $ep$ data is presented; simultaneous fits of parton distribution functions together with contributions of "new physics" processes were performed. Results are presented considering a finite radius of quarks within the quark form-factor model. The resulting 95% C.L. upper limit on the effective quark radius is $0.43\cdot 10^{-16}$ cm.Comment: 10 pages, 4 figures, accepted by Phys. Lett.