Mutations in human immunodeficiency virus type 1 reverse transcriptase that make it sensitive to degradation by the viral protease in virions are selected against in patients

AbstractMutations in the thumb subdomain of reverse transcriptase (RT) of HIV-1 can cause this enzyme to be degraded in virions by the viral protease (PR). Many of these mutations confer a temperature-sensitive phenotype on RT and viral replication. The degradation of RT by PR appears to take place after Gag-Pol has been processed. We show here that mutations in other parts of RT, including the RNase H domain, can make RT PR-sensitive and temperature-sensitive. These data explain why some mutations in the RNase H domain, which had little or no effect on the polymerase activity of purified recombinant RT, had a profound effect on viral titer. Because the PR-sensitive phenotype significantly reduced viral titer, we previously suggested that these mutations would be selected against in patients. We also show that RT mutations that are known to confer a temperature sensitive phenotype are rarely found in the Stanford database

Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis

AbstractMethionine at position 184 of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) was changed to valine, isoleucine, threonine, or alanine in an HIV-1-based vector. The vectors were analyzed for replication capacity and for resistance to the nucleoside analog 2′,3′-dideoxy-3′thiacytidine (3TC) using a single-cycle assay. Viruses containing the valine or isoleucine mutations were highly resistant to 3TC and replicated almost as well as the wild-type virus. The virus containing the threonine mutation was resistant to 3TC, but replicated about 30% as well as the wild-type. The alanine mutation conferred partial resistance to 3TC, but replicated poorly. The amounts of viral DNA synthesized decreased in 3TC-treated cells when the cells were infected with wild-type virus and the M184A mutant. The effect of these mutations on the generation of the ends of the linear viral DNA was determined using the sequence of the 2-LTR circle junctions. The M184T mutation increased the proportion of 2-LTR circle junctions containing a tRNA insertion, suggesting that the mutation affected the RNase H activity of RT

GPUVerify: A Verifier for GPU Kernels

We present a technique for verifying race- and divergence-freedom of GPU kernels that are written in mainstream ker-nel programming languages such as OpenCL and CUDA. Our approach is founded on a novel formal operational se-mantics for GPU programming termed synchronous, delayed visibility (SDV) semantics. The SDV semantics provides a precise definition of barrier divergence in GPU kernels and allows kernel verification to be reduced to analysis of a sequential program, thereby completely avoiding the need to reason about thread interleavings, and allowing existing modular techniques for program verification to be leveraged. We describe an efficient encoding for data race detection and propose a method for automatically inferring loop invari-ants required for verification. We have implemented these techniques as a practical verification tool, GPUVerify, which can be applied directly to OpenCL and CUDA source code. We evaluate GPUVerify with respect to a set of 163 kernels drawn from public and commercial sources. Our evaluation demonstrates that GPUVerify is capable of efficient, auto-matic verification of a large number of real-world kernels

Human Engineering of Space Vehicle Displays and Controls

Proper attention to the integration of the human needs in the vehicle displays and controls design process creates a safe and productive environment for crew. Although this integration is critical for all phases of flight, for crew interfaces that are used during dynamic phases (e.g., ascent and entry), the integration is particularly important because of demanding environmental conditions. This panel addresses the process of how human engineering involvement ensures that human-system integration occurs early in the design and development process and continues throughout the lifecycle of a vehicle. This process includes the development of requirements and quantitative metrics to measure design success, research on fundamental design questions, human-in-the-loop evaluations, and iterative design. Processes and results from research on displays and controls; the creation and validation of usability, workload, and consistency metrics; and the design and evaluation of crew interfaces for NASA's Crew Exploration Vehicle are used as case studies

Why Do HIV-1 and HIV-2 Use Different Pathways to Develop AZT Resistance?

The human immunodeficiency virus type 1 (HIV-1) develops resistance to all available drugs, including the nucleoside analog reverse transcriptase inhibitors (NRTIs) such as AZT. ATP-mediated excision underlies the most common form of HIV-1 resistance to AZT. However, clinical data suggest that when HIV-2 is challenged with AZT, it usually accumulates resistance mutations that cause AZT resistance by reduced incorporation of AZTTP rather than selective excision of AZTMP. We compared the properties of HIV-1 and HIV-2 reverse transcriptase (RT) in vitro. Although both RTs have similar levels of polymerase activity, HIV-1 RT more readily incorporates, and is more susceptible to, inhibition by AZTTP than is HIV-2 RT. Differences in the region around the polymerase active site could explain why HIV-2 RT incorporates AZTTP less efficiently than HIV-1 RT. HIV-1 RT is markedly more efficient at carrying out the excision reaction with ATP as the pyrophosphate donor than is HIV-2 RT. This suggests that HIV-1 RT has a better nascent ATP binding site than HIV-2 RT, making it easier for HIV-1 RT to develop a more effective ATP binding site by mutation. A comparison of HIV-1 and HIV-2 RT shows that there are numerous differences in the putative ATP binding sites that could explain why HIV-1 RT binds ATP more effectively. HIV-1 RT incorporates AZTTP more efficiently than does HIV-2 RT. However, HIV-1 RT is more efficient at ATP-mediated excision of AZTMP than is HIV-2 RT. Mutations in HIV-1 RT conferring AZT resistance tend to increase the efficiency of the ATP-mediated excision pathway, while mutations in HIV-2 RT conferring AZT resistance tend to increase the level of AZTTP exclusion from the polymerase active site. Thus, each RT usually chooses the pathway best suited to extend the properties of the respective wild-type enzymes

Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site

AbstractComparison of the recently solved structure of HIV-1reverse transcriptase (RT)-DNA-dNTP ternary complex with the previously solved structure of RT-DNA binary complex suggests mechanisms by which the HIV-1 RT becomes resistant to nucleoside-analog inhibitors, drugs currently used in the treatment of AIDS

On the metallicity dependence of crystalline silicates in oxygen-rich asymptotic giant branch stars and red supergiants

We investigate the occurrence of crystalline silicates in oxygen-rich evolved stars across a range of metallicities and mass-loss rates. It has been suggested that the crystalline silicate feature strength increases with increasing mass-loss rate, implying a correlation between lattice structure and wind density. To test this, we analyse Spitzer IRS and Infrared Space Observatory SWS spectra of 217 oxygen-rich asymptotic giant branch stars and 98 red supergiants in the Milky Way, the Large and Small Magellanic Clouds and Galactic globular clusters. These encompass a range of spectral morphologies from the spectrally-rich which exhibit a wealth of crystalline and amorphous silicate features to 'naked' (dust-free) stars. We combine spectroscopic and photometric observations with the GRAMS grid of radiative transfer models to derive (dust) mass-loss rates and temperature. We then measure the strength of the crystalline silicate bands at 23, 28 and 33 microns. We detect crystalline silicates in stars with dust mass-loss rates which span over 3 dex, down to rates of ~10^-9 solar masses/year. Detections of crystalline silicates are more prevalent in higher mass-loss rate objects, though the highest mass-loss rate objects do not show the 23-micron feature, possibly due to the low temperature of the forsterite grains or it may indicate that the 23-micron band is going into absorption due to high column density. Furthermore, we detect a change in the crystalline silicate mineralogy with metallicity, with enstatite seen increasingly at low metallicity.Comment: Accepted for publication in MNRAS, 24 pages, 16 figure

Trends in Clinical, Demographic, and Biochemical Characteristics of Patients with Acute Myocardial Infarction from 2003 to 2008: A Report from the American Heart Association Get with the Guidelines Coronary Artery Disease Program

Background: An analysis of the changes in the clinical and demographic characteristics of patients with acute myocardial infarction could identify successes and failures of risk factor identification and treatment of patients at increased risk for cardiovascular events. Methods and results: We reviewed data collected from 138 122 patients with acute myocardial infarction admitted from 2003 to 2008 to hospitals participating in the American Heart Association Get With The Guidelines Coronary Artery Disease program. Clinical, demographic, and laboratory characteristics were analyzed for each year stratified on the electrocardiogram at presentation. Patients with non–ST-segment–elevation myocardial infarction were older, more likely to be women, and more likely to have hypertension, diabetes mellitus, and a history of past cardiovascular disease than were patients with ST-elevation myocardial infarction. In the overall patient sample, significant trends were observed of an increase over time in the proportions of non–ST-segment–elevation myocardial infarction, patient age of 45 to 65 years, obesity, and female sex. The prevalence of diabetes mellitus decreased over time, whereas the prevalences of hypertension and smoking were substantial and unchanging. The prevalence of “low” high-density lipoprotein increased over time, whereas that of “high” low-density lipoprotein decreased. Stratum-specific univariate analysis revealed quantitative and qualitative differences between strata in time trends for numerous demographic, clinical, and biochemical measures. On multivariable analysis, there was concordance between strata with regard to the increase in prevalence of patients 45 to 65 years of age, obesity, and “low” high-density lipoprotein and the decrease in prevalence of “high” low-density lipoprotein. However, changes in trends in age distribution, sex ratio, and prevalence of smokers and the magnitude of change in diabetes mellitus prevalence differed between strata. Conclusions: There were notable differences in risk factors and patient characteristics among patients with ST-elevation myocardial infarction and those with non–ST-segment–elevation myocardial infarction. The increasing prevalence of dysmetabolic markers in a growing proportion of patients with acute myocardial infarction suggests further opportunities for risk factor modification

Images of survival, stories of destruction: Nuclear war on British screens from 1945 to the early 1960s

This article discusses a range of depictions and discussions of nuclear war, which appeared on British screens in the first half of the Cold War, in order to understand the changing way nuclear weapons were viewed within British culture. Using such screened images to understand how nuclear war was constructed and represented within British culture, the article argues that the hydrogen bomb, not the atomic bomb, was the true harbinger of the nuclear revolution that transformed cultural understandings of warfare and destruction. Although the atomic bomb created a great deal of anxiety within British popular culture, representations of atomic attack elided atomic destruction with that experienced in 1939-45, emphasising the 'survivability' of atomic war. In the thermonuclear era, the Second World War could not undertake the same symbolic work. The image of the city-destroying bomb was an imaginative as well as technological step-change. Screened representations stressed that a thermonuclear war would literally end the world. As such, they preceded, and indeed provided the cultural climate for, the rise of the Campaign for Nuclear Disarmament (CND). The Campaign exploited and further popularised this idea of the apocalyptic nuclear war as a key aspect of its political and moral standpoint. The article concludes, however, that the cultural hegemony of this vision of nuclear war equally helped underpin notions of nuclear deterrence. The basic assumptions about the nature of nuclear war constructed and circulated on British screens therefore formed part of CND's 'cultural' victory but the article also explains why this did not translate into the political realm. © Edinburgh University Press