The evolution of drug resistance in HIV has been a major obstacle in combating the AIDS epidemic, and development of the next generation of antiviral drugs will depend on improvements in the methodology addressing resistance. This work examines HIV evolution from a structural perspective, focusing on the development of methods to anticipate drug resistance and improve drug discovery efforts. To understand the evolution of HIV in the presence of inhibitors requires knowledge of viral replication capacity as well as drug resistance. Replication capacity can be predicted with a phylogenetic approach, which estimates impairment in HIV protease activity. Pairing these estimates with a structural model based on molecular docking allows the detection of most major clinically observed protease mutations. Combining structural modeling and analysis of existing protease mutations generates predictions of drug resistance mutations for an experimental protease inhibitor. Mutagenesis experiments validate these predictions, while also revealing epistatic interactions and cross-resistance with existing inhibitors. A fitness model based on predicted replication capacity and drug resistance is able to rank in vitro HIV mutant infectivity with significant accuracy. This fitness model is incorporated into a simulation of viral evolution, which correlates with clinically observed mutation prevalence. Simulations also affirm the high level of cross-resistance among protease inhibitors, highlighting the importance of alternative drug targets. Current drug discovery projects often use computer-based models of protein-ligand interaction for docking and virtual screening. A novel analysis of binding energy results from large-scale virtual screening identifies representative wild-type and mutant protease structures, focusing future efforts. Complementary efforts in the study of APS reductase reveal correlations between the distribution docking results and the underlying energy surface. Cluster analysis is shown to be an empirical measure of docking entropy which can improve the accuracy of binding energy predictions. Applying these insights in a virtual screen for new inhibitors of HIV protease, a library of 1,585 compounds is narrowed to 36 candidates. Five of these compounds prove to be inhibitors. Modeling indicates that two of them bind outside the protease active site, suggesting potential leads for a new class of protease inhibitor

Community health centers (CHCs) are a cornerstone of the health care safety net. They are the primary source of care for many low-income populations, including both those newly insured under the Affordable Care Act (ACA) and those who were left out and will remain uninsured. The ACA provides challenges and opportunities for CHCs, which will require significant changes in infrastructure and care delivery approaches to meet those challenges. This policy brief assesses the progress made by CHCs in Los Angeles County in meeting a number of key indicators of ACA readiness in early 2014. The authors find that 39 percent of CHCs are well prepared, 23 percent have made some progress, and the rest are at the initial phases of preparation and/or lack adequate resources to meet the requirements. The latter group of CHCs require help to embark on strategic improvements in infrastructure and care delivery.

Objective

To estimate the tobacco-attributable costs of diseases separately for smoked and smokeless tobacco use in India.

Methods

The prevalence-based attributable-risk approach was used to estimate the economic cost of tobacco using healthcare expenditure data from the National Sample Survey, a nationally representative household sample survey conducted in India in 2004. Four major categories of tobacco-related disease-tuberculosis, respiratory diseases, cardiovascular diseases and neoplasms-were considered.

Results

Direct medical costs of treating tobacco related diseases in India amounted to $907 million for smoked tobacco and $285 million for smokeless tobacco. The indirect morbidity costs of tobacco use, which includes the cost of caregivers and value of work loss due to illness, amounted to $398 million for smoked tobacco and $104 million for smokeless tobacco. The total economic cost of tobacco use amounted to $1.7 billion. Tuberculosis accounted for 18% of tobacco-related costs ($311 million) in India. Of the total cost of tobacco, 88% was attributed to men.

Conclusions

The cost of tobacco use was many times more than the expenditures on tobacco control by the government of India and about 16% more than the total tax revenue from tobacco. The tobacco-attributable cost of tuberculosis was three times higher than the expenditure on tuberculosis control in India. The economic costs estimated here do not include the costs of premature mortality from tobacco use, which is known to comprise roughly 50% to 80% of the total economic cost of tobacco in many countries.

More than 70 percent of behavioral health conditions are first diagnosed in the primary care setting. Yet physical and behavioral health care are typically provided separately, compelling many vulnerable patients to navigate the complexities of two separate systems of care. This policy brief examines five community health centers (CHCs) in California that have taken preliminary steps toward creating "one-stop shopping" for both physical and behavioral health care. The steps taken to increase integration by the CHCs include employing behavioral health providers, using a single electronic health record that includes both physical and behavioral health data, transforming the physical space, and developing mechanisms for effective transition of patients between providers. The findings emphasize the importance of changes to Medi-Cal reimbursement policies to promote same-day visits, as well as the importance of cultural changes to integrate behavioral health. They also highlight the need for comprehensive tools to assess and promote integration and to identify solutions for the most challenging activities required to achieve full integration.

The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.

HMO enrollees with limited English proficiency, and particularly those in fair to poor health, face communication barriers despite language assistance regulations. More than 1.3 million California HMO enrollees ages 18 to 64 do not speak English well enough to communicate with medical providers and may experience reduced access to high-quality health care if they do not receive appropriate language assistance services. Based on analysis of the 2007 and 2009 California Health Interview Surveys (CHIS), commercial HMO enrollees with limited English proficiency (LEP) in poorer health are more likely to have difficulty understanding their doctors, placing this already vulnerable population at even greater risk. The analysis also uses CHIS to examine the potential impact of health plan monitoring starting in 2009 (due to a 2003 amendment to the Knox-Keene Health Care Services Act) requiring health plans to provide free qualified interpretation and translation services to HMO enrollees. The authors recommend that California’s health plans continue to incorporate trained interpreters into their contracted networks and delivery systems, paying special attention to enrollees in poorer health. The results may serve as a planning tool for health plans, providing a detailed snapshot of enrollee characteristics that will help design effective programs now and prepare for a likely increase in insured LEP populations in the future, as full implementation of the Affordable Care Act takes place over the next decade.