A New Biophysical Metric for Interrogating the Information Content in Human Genome Sequence Variation: Proof of Concept

Various studies have shown an association between single nucleotide polymorphisms (SNPs) and common disease. We hypothesize that information encoded in the structure of SNP haploblock variation illumines molecular pathways and cellular mechanisms involved in the regulation of host adaptation to the environment. We developed and utilized the normalized information content (NIC), a novel metric based on SNP haploblock variation. We found that all SNP haploblocks with statistically low information content contained putative transcription factor binding sites and microRNA motifs. We were able to translate a biophysical, mathematical measure of common variants into a deeper understanding of the life sciences through analysis of biochemical patterns associated with SNP haploblock variation. We submit that this new metric, NIC, may be useful in decoding the functional significance of common variation in the human genome and in analyzing the regulation of molecular pathways involved in host adaptation to environmental pathogens.Comment: 13 page

Condom use and incarceration among STI clinic attendees in the Deep South

Abstract Background Incarceration history is associated with lower rates of condom use and increased HIV risk. Less is known about duration of incarceration and multiple incarcerations’ impact on condom use post-release. Methods In the current study, we surveyed 1,416 adults in Mississippi about their incarceration history and sexual risk behaviors. Generalized estimating equations (GEE) were used to test associations between duration of incarceration, multiple incarcerations, socio-demographic factors, substance use, sexual behavior, and event level condom use at last sex. Results After adjusting for covariates, having been incarcerated for at least 6 months two or more times remained significantly associated with condomless sex. Conclusions This study found a strong, independent relationship between condom use and multiple, long-term incarceration events among patients in an urban STI clinic in the Deep South. The results suggest that duration of incarceration and multiple incarcerations have significant effects on sexual risk behaviors, underscoring the deleterious impact of long prison or jail sentences on population health. Our findings also suggest that correctional health care professionals and post-release providers might consider offering comprehensive sexual and reproductive health services and those providing community care should consider screening for previous incarceration as a marker of risk

Tuberculosis control among substance users: The indigenous leadership outreach model vs. standard care.

Tuberculosis control among substance users: The indigenous leadership outreach model vs. standard care

Estimating the burden of tuberculosis among foreign-born persons acquired prior to entering the U.S., 2005-2009.

BACKGROUND: The true burden of reactivation of remote latent tuberculosis infection (reactivation TB) among foreign-born persons with tuberculosis (TB) within the United States is not known. Our study objectives were to estimate the proportion of foreign-born persons with TB due reactivation TB and to describe characteristics of foreign-born persons with reactivation TB. METHODS: We conducted a cross-sectional study of patients with an M. tuberculosis isolate genotyped by the U.S. National TB Genotyping Service, 2005-2009. TB cases were attributed to reactivation TB if they were not a member of a localized cluster of cases. Localized clusters were determined by a spatial scan statistic of cases with isolates with matching TB genotype results. Crude odds ratios and 95% confidence intervals were used to assess relations between reactivation TB and select factors among foreign-born persons. MAIN RESULTS: Among the 36,860 cases with genotyping and surveillance data reported, 22,151 (60%) were foreign-born. Among foreign-born persons with TB, 18,540 (83.7%) were attributed to reactivation TB. Reactivation TB among foreign-born persons was associated with increasing age at arrival, incidence of TB in the country of origin, and decreased time in the U.S. at the time of TB diagnosis. CONCLUSIONS: Four out of five TB cases among foreign-born persons can be attributed to reactivation TB and present the largest challenge to TB elimination in the U.S. TB control strategies among foreign-born persons should focus on finding and treating latent tuberculosis infection prior to or shortly after arrival to the United States and on reducing the burden of LTBI through improvements in global TB control

Proportion of reactivation TB among foreign-born TB cases by estimated annual TB incidence in the country of origin, United States 2005–2009.

1<p>Column percent.</p>2<p>per 100,000 population.</p

Proportion of reactivation TB among foreign-born TB cases by time in the U.S. prior to TB diagnosis, United States 2005–2009.

1<p>Column percent.</p>2<p>Comparing nonclustered to clustered.</p