Explore the vast range of titles available.

We describe a new, state‐of‐the‐art, Earth System Regional Climate Model (RegCM‐ES), which includes the coupling between the atmosphere, ocean, and land surface, as well as a hydrological and ocean biogeochemistry model, with the capability of using a variety of physical parameterizations. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains and more regional settings featuring climatically important coupled phenomena. Regional coupled ocean‐atmosphere models can be especially useful tools to provide information on the mechanisms of air‐sea interactions and feedbacks occurring at fine spatial and temporal scales. RegCM‐ES shows a good representation of precipitation and SST fields over the domains tested, as well as realistic simulations of coupled air‐sea processes and interactions. The RegCM‐ES model, which can be easily implemented over any regional domain of interest, is open source, making it suitable for usage by the broad scientific community. Plain Language Summary The increasing availability of observational data sets of high temporal and spatial resolution is providing a more complete view of the ocean and atmosphere, revealing strong air‐sea coupling processes. In order to obtain an accurate representation and better understanding of the climate system, its variability, and possible future change, the inclusion of all mechanisms of interaction among the different climate components becomes ever more desirable. Regional coupled ocean‐atmosphere models can be especially useful tools to provide information on the mechanisms of air‐sea interactions and feedback occurring at regional fine spatial and temporal scales. Here we present a new, state‐of‐the‐art, Earth System Regional Climate Model (RegCM‐ES). Key Points A new Regional Earth System Model (RegCM‐ES) successfully simulates climate features in regions where coupled air‐sea processes are important RegCM‐ES shows reduction of precipitation biases and good performance simulating the effects of air‐sea interactions over frontal regions RegCM‐ES is an open source community model, making it suitable for use by a large scientific community on any regional domain of interest

We describe a new, state‐of‐the‐art, Earth System Regional Climate Model (RegCM‐ES), which includes the coupling between the atmosphere, ocean, and land surface, as well as a hydrological and ocean biogeochemistry model, with the capability of using a variety of physical parameterizations. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains and more regional settings featuring climatically important coupled phenomena. Regional coupled ocean‐atmosphere models can be especially useful tools to provide information on the mechanisms of air‐sea interactions and feedbacks occurring at fine spatial and temporal scales. RegCM‐ES shows a good representation of precipitation and SST fields over the domains tested, as well as realistic simulations of coupled air‐sea processes and interactions. The RegCM‐ES model, which can be easily implemented over any regional domain of interest, is open source, making it suitable for usage by the broad scientific community. The increasing availability of observational data sets of high temporal and spatial resolution is providing a more complete view of the ocean and atmosphere, revealing strong air‐sea coupling processes. In order to obtain an accurate representation and better understanding of the climate system, its variability, and possible future change, the inclusion of all mechanisms of interaction among the different climate components becomes ever more desirable. Regional coupled ocean‐atmosphere models can be especially useful tools to provide information on the mechanisms of air‐sea interactions and feedback occurring at regional fine spatial and temporal scales. Here we present a new, state‐of‐the‐art, Earth System Regional Climate Model (RegCM‐ES). A new Regional Earth System Model (RegCM‐ES) successfully simulates climate features in regions where coupled air‐sea processes are important RegCM‐ES shows reduction of precipitation biases and good performance simulating the effects of air‐sea interactions over frontal regions RegCM‐ES is an open source community model, making it suitable for use by a large scientific community on any regional domain of interest

Tigr flu survey Published on 5 October online, the in-print version of the survey of more than 200 influenza virus sequences by The Institute for Genomic Research appears this week. Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality 1 , 2 . The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 ‘Spanish’ flu, one of the most deadly outbreaks in recorded history, which killed 30–50 million people worldwide, the 1957 ‘Asian’ flu, and the 1968 ‘Hong Kong’ flu 3 . Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.

A recent collaboration between federal, state and private partners in southeast Oregon developed mental models to distill complex plant-based community ecology for management. The mental models were then turned into a simplified, habitat-classification system that addressed landscape-level threats to the sagebrush ecosystem. The simplified, habitat-classification system formed the foundation of Threat-based State and Transition Models (TBSTM). We quantitatively linked greater sage-grouse (Centrocercus urophasianus, hereafter sage-grouse) lek occurrence to a landscape-level habitat classification based upon the TBSTM framework. We investigated whether TBSTM classifications were able to spatially predict locations of sage-grouse breeding areas equivalently to landcover variables that have been studied for over a decade. We showed the TBSTM framework was able to predict the locations of sage-grouse accurately (R² = 0.70, AUC = 0.91, Correctly Classified = 83%). Model fit statistics were similar to the model built with traditional land cover variables (R² = 0.65, AUC = 0.89, Correctly Classified = 80%). The high degree of model fit for the TBSTM framework allows conservation practitioners a direct, quantifiable, and biological link to understand outcomes of transitioning habitats from various threat states to sagebrushdominated landscapes with a perennial understory across large landscapes. Sage-grouse are well known to respond to landscape-level amounts of habitat and exhibit low tolerance to threats. We documented similar responses between threats such as the percentage of conifers within 560-m and the conifer threat bin at the same spatial scale. Our work also quantified the importance of having a healthy perennial-grass understory and perennial-grass patches in conjunction with sagebrush cover across large landscapes. Our work suggests that understory grass communities at landscape scales may be limiting grouse occurrence in certain parts of Oregon.

A phase II efficacy trial was conducted with recombinant human immunodeficiency virus (HIV) type 1 envelope glycoprotein gp160 (rgp160) in 608 HIV-infected, asymptomatic volunteers with CD4+ cell counts >400 cells/mm3. During a 5-year study, volunteers received a 6-shot primary series of immunizations with either rgp160 or placebo over 6 months, followed by booster immunizations every 2 months. Repeated vaccination with rgp160 was safe and persistently immunogenic. Adequate follow-up and acquisition of endpoints allowed for definitive interpretation of the trial results. There was no evidence that rgp160 has efficacy as a therapeutic vaccine in early-stage HIV infection, as measured at primary endpoints (50% decline in CD4+ cell count or disease progression to Walter Reed stage 4, 5, or 6) or secondary endpoints. A transient improvement was seen in the secondary CD4 endpoint for the vaccination compared with the placebo arm, but this did not translate into improved clinical outcome.

A phase II efficacy trial was conducted with recombinant human immunodeficiency virus (HIV) type 1 envelope glycoprotein gp160 (rgp160) in 608 HIV-infected, asymptomatic volunteers with CD4+ cell counts >400 cells/mm3. During a 5-year study, volunteers received a 6-shot primary series of immunizations with either rgp160 or placebo over 6 months, followed by booster immunizations every 2 months. Repeated vaccination with rgp160 was safe and persistently immunogenic. Adequate follow-up and acquisition of endpoints allowed for definitive interpretation of the trial results. There was no evidence that rgp160 has efficacy as a therapeutic vaccine in early-stage HIV infection, as measured at primary endpoints (50% decline in CD4+ cell count or disease progression to Walter Reed stage 4, 5, or 6) or secondary endpoints. A transient improvement was seen in the secondary CD4 endpoint for the vaccination compared with the placebo arm, but this did not translate into improved clinical outcome.

Systems for the staging of individuals with human immunodeficiency virus type 1 (HIV-1) infection were developed 15 years ago. Subsequently, assays for quantitating HIV-1 RNA and immunophenotyping of lymphocyte subsets have been developed and validated. The utility of these assays for improved staging in early disease was evaluated in 256 HIV-infected adults (52% minority) with CD4 counts > or = 400 cells/microL followed in U.S. military medical centers before the highly active anti-retroviral therapy era. HIV viral load (RNA) was quantitated; the frequencies of select CD4+ immunophenotypes were determined in 112 subjects. The results were analyzed in relation to three outcome measures: death, first acquired immunodeficiency syndrome-defining opportunistic infection, and CD4 count < or = 200 cells/microL. Serum RNA level and CD4 count were each found to be predictive of all three outcomes. In addition, increases in the T-cell subsets CD28-CD4+ and CD29+CD26-CD4+ were found to be independently predictive of more rapid progression. The classification of early-stage HIV patients is improved by the quantitation of both viral RNA and T-lymphocyte subsets.