Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

HIV Testing, Subjective Beliefs and Economic Behavior.

This paper examines the effects of learning HIV status on economic behavior among rural Malawians. According to economic life-cycle models, if learning HIV results is informative about additional years of life, being diagnosed HIV-positive or negative should predict changes in consumption, investment and savings behavior with important micro and macro-economic implications. Using an experiment that randomly assigned incentives to learn HIV results, I find that while learning HIV results had short term effects on subjective belief of HIV infection, these differences did not persist after two years. Consistent with this, there were relatively few differences two years later in savings, income, expenditures, and employment between those who learned and did not learn their status.

Social security health insurance for the informal sector in Nicaragua: a randomized evaluation.

This article presents the results from an experimental evaluation of a voluntary health insurance program for informal sector workers in Nicaragua. Costs of the premiums as well as enrollment location were randomly allocated. Overall, take-up of the program was low, with only 20% enrollment. Program costs and streamlined bureaucratic procedures were important determinants of enrollment. Participation of local microfinance institutions had a slight negative effect on enrollment. One year later, those who received insurance substituted toward services at covered facilities and total out-of-pocket expenditures fell. However, total expenditures fell by less than the insurance premiums. We find no evidence of an increase in health-care utilization among the newly insured. We also find very low retention rates after the expiration of the subsidy, with less than 10% of enrollees still enrolled after one year. To shed light on the findings from the experimental results, we present qualitative evidence of institutional and contextual factors that limited the success of this program.

Comprehensive T cell repertoire characterization of non-small cell lung cancer.

Immunotherapy targeting T cells is increasingly utilized to treat solid tumors including non-small cell lung cancer (NSCLC). This requires a better understanding of the T cells in the lungs of patients with NSCLC. Here, we report T cell repertoire analysis in a cohort of 236 early-stage NSCLC patients. T cell repertoire attributes are associated with clinicopathologic features, mutational and immune landscape. A considerable proportion of the most prevalent T cells in tumors are also prevalent in the uninvolved tumor-adjacent lungs and appear specific to shared background mutations or viral infections. Patients with higher T cell repertoire homology between the tumor and uninvolved tumor-adjacent lung, suggesting a less tumor-focused T cell response, exhibit inferior survival. These findings indicate that a concise understanding of antigens and T cells in NSCLC is needed to improve therapeutic efficacy and reduce toxicity with immunotherapy, particularly adoptive T cell therapy.

Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma.

There has been a dramatic increase in the detection of lung nodules, many of which are preneoplasia atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) or invasive adenocarcinoma (ADC). The molecular landscape and the evolutionary trajectory of lung preneoplasia have not been well defined. Here, we perform multi-region exome sequencing of 116 resected lung nodules including AAH (n = 22), AIS (n = 27), MIA (n = 54) and synchronous ADC (n = 13). Comparing AAH to AIS, MIA and ADC, we observe progressive genomic evolution at the single nucleotide level and demarcated evolution at the chromosomal level supporting the early lung carcinogenesis model from AAH to AIS, MIA and ADC. Subclonal analyses reveal a higher proportion of clonal mutations in AIS/MIA/ADC than AAH suggesting neoplastic transformation of lung preneoplasia is predominantly associated with a selective sweep of unfit subclones. Analysis of multifocal pulmonary nodules from the same patients reveal evidence of convergent evolution.

The Demand for, and Impact of, Learning HIV Status.

This paper evaluates an experiment in which individuals in rural Malawi were randomly assigned monetary incentives to learn their HIV results after being tested. Distance to the HIV results centers was also randomly assigned. Without any incentive, 34 percent of the participants learned their HIV results. However, even the smallest incentive doubled that share. Using the randomly assigned incentives and distance from results centers as instruments for the knowledge of HIV status, sexually active HIV-positive individuals who learned their results are three times more likely to purchase condoms two months later than sexually active HIV-positive individuals who did not learn their results; however, HIV-positive individuals who learned their results purchase only two additional condoms than those who did not. There is no significant effect of learning HIV-negative status on the purchase of condoms.

Genomic and immune heterogeneity are associated with differential responses to therapy in melanoma.

Appreciation for genomic and immune heterogeneity in cancer has grown though the relationship of these factors to treatment response has not been thoroughly elucidated. To better understand this, we studied a large cohort of melanoma patients treated with targeted therapy or immune checkpoint blockade (n = 60). Heterogeneity in therapeutic responses via radiologic assessment was observed in the majority of patients. Synchronous melanoma metastases were analyzed via deep genomic and immune profiling, and revealed substantial genomic and immune heterogeneity in all patients studied, with considerable diversity in T cell frequency, and few shared T cell clones (<8% on average) across the cohort. Variables related to treatment response were identified via these approaches and through novel radiomic assessment. These data yield insight into differential therapeutic responses to targeted therapy and immune checkpoint blockade in melanoma, and have key translational implications in the age of precision medicine.

Cohort Profile: The Malawi Longitudinal Study of Families and Health (MLSFH).

The Malawi Longitudinal Study of Families and Health (MLSFH) is one of very few long-standing, publicly available longitudinal cohort studies in a sub-Saharan African (SSA) context. It provides a rare record of more than a decade of demographic, socioeconomic and health conditions in one of the world's poorest countries. The MLSFH was initially established in 1998 to study social network influences on fertility behaviours and HIV risk perceptions, and over time the focus of the study expanded to include health, sexual behaviours, intergenerational relations and family/household dynamics. The currently available data include MLSFH rounds collected in 1998, 2001, 2004, 2006, 2008, 2010 and 2012 for up to 4000 individuals, providing information about socioeconomic and demographic characteristics, sexual behaviours, marriage, household/family structure, risk perceptions, social networks and social capital, intergenerational relations, HIV/AIDS and other dimensions of health. The MLSFH public use data can be requested on the project website: http://www.malawi.pop.upenn.edu/.

Perceptions of Male Circumcision among Married Couples in Rural Malawi.

Voluntary medical male circumcision (VMMC) is being suggested as an essential HIV prevention strategy in high-prevalence areas. These analyses reflect data collected from 360 married couples, 50% of which included a circumcised husband and the other 50% uncircumcised, in rural Malawi. Regardless of their circumcision status, men were more likely to perceive that being circumcised was less painful than having a tooth pulled, giving birth, and having malaria. Men reported having the same sexual pleasure regardless of the circumcision status, while women were 2.0 times more likely to report greater sexual pleasure with a circumcised partner. Participants identified the medical benefits of VMMC and highlighted the potential personal benefits of VMMC. As VMMC has become a promising method of HIV prevention, this study revealed opportunities for intervention development to increase rates of VMMC among men.

PREVALENCE OF AND FACTORS ASSOCIATED WITH ORAL SEX AMONG RURAL AND URBAN MALAWIAN MEN.

Despite medical evidence that female-to-male oral sex (fellatio) carries a lower risk for HIV transmission than unprotected vaginal intercourse, little research exists on the practice of fellatio in Africa. We used two samples of men from Malawi-one rural and one urban-to examine the prevalence of oral sex. While 97% of the rural sample and 87% of the urban sample reported having had vaginal sex, just 2% and 12%, respectively, said they had ever received oral sex. Only half of the rural sample, and less than three quarters of the urban sample, reported having heard of oral sex. Education, exposure to newspapers and television, and condom use significantly predicted oral sex knowledge after controlling for other confounding factors, while exposure to radio did not. The large gap between sexual activity and oral sex prevalence suggests that fellatio should be taken into consideration as a potential component of an HIV prevention strategy, but further quantitative and qualitative research that includes women as well as men is needed to understand potential benefits and drawbacks.

Increasing the acceptability of HIV counseling and testing with three C's: convenience, confidentiality and credibility.

Agencies engaged in humanitarian efforts to prevent the further spread of HIV have emphasized the importance of voluntary counseling and testing (VCT), and most high-prevalence countries now have facilities that offer testing free of charge. The utilization of these services is disappointingly low, however, despite high numbers reporting that they would like to be tested. Explanations of this discrepancy typically rely on responses to hypothetical questions posed in terms of psychological or social barriers; often, the explanation is that people fear learning that they are infected with a disease that they understand to be fatal and stigmatizing. Yet when we offered door-to-door rapid blood testing for HIV as part of a longitudinal study in rural Malawi, the overwhelming majority agreed to be tested and to receive their results immediately. Thus, in this paper, we ask: why are more people not getting tested? Using an explanatory research design, we find that rural Malawians are responsive to door-to-door HIV testing for the following reasons: it is convenient, confidential, and the rapid blood test is credible. Our study suggests that attention to these factors in VCT strategies may mitigate the fear of HIV testing, and ultimately increase uptake in rural African settings.