Los Alamos National Laboratory

About: Los Alamos National Laboratory is a facility organization based out in Los Alamos, New Mexico, United States. It is known for research contribution in the topics: Neutron & Laser. The organization has 31079 authors who have published 74688 publications receiving 2999590 citations. The organization is also known as: LANL & Project Y.

The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy.

Abstract: Replication-competent HIV-1 can be isolated from infected patients despite prolonged plasma virus suppression by anti-retroviral treatment1,2,3. Recent studies have identified resting, memory CD4+ T lymphocytes as a long-lived latent reservoir of HIV-1 (refs. 4,5). Cross-sectional analyses indicate that the reservoir is rather small, between 103 and 107 cells per patient5,6. In individuals whose plasma viremia levels are well suppressed by anti-retroviral therapy, peripheral blood mononuclear cells containing replication-competent HIV-1 were found to decay with a mean half-life of approximately 6 months7, close to the decay characteristics of memory lymphocytes in humans and monkeys8,9,10. In contrast, little decay was found in a less-selective patient population11. We undertook this study to address this apparent discrepancy. Using a quantitative micro-culture assay, we demonstrate here that the latent reservoir decays with a mean half-life of 6.3 months in patients who consistently maintain plasma HIV-1 RNA levels of fewer than 50 copies/ml. Slower decay rates occur in individuals who experience intermittent episodes of plasma viremia. Our findings indicate that the persistence of the latent reservoir of HIV-1 despite prolonged treatment is due not only to its slow intrinsic decay characteristics but also to the inability of current drug regimens to completely block HIV-1 replication.

Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction

Abstract: We introduce a distance-based phylogeny reconstruction method called ‘‘weighted neighbor joining,’’ or ‘‘Weighbor’’ for short. As in neighbor joining, two taxa are joined in each iteration; however, the Weighbor criterion for choosing a pair of taxa to join takes into account that errors in distance estimates are exponentially larger for longer distances. The criterion embodies a likelihood function on the distances, which are modeled as correlated Gaussian random variables with different means and variances, computed under a probabilistic model for sequence evolution. The Weighbor criterion consists of two terms, an additivity term and a positivity term, that quantify the implications of joining the pair. The first term evaluates deviations from additivity of the implied external branches, while the second term evaluates confidence that the implied internal branch has a positive branch length. Compared with maximum-likelihood phylogeny reconstruction, Weighbor is much faster, while building trees that are qualitatively and quantitatively similar. Weighbor appears to be relatively immune to the ‘‘long branches attract’’ and ‘‘long branch distracts’’ drawbacks observed with neighbor joining, BIONJ, and parsimony.

Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin.

Abstract: Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore N-linked glycosylation site (sequon) variation at the population level in these viruses, using a new Web-based program developed to facilitate the sequon tracking and to define patterns (www.hiv.lanl.gov). This tool allowed rapid visualization of the two distinctive patterns of sequon variation found in HIV-1, HIV-2, and SIV CPZ. The first pattern (fixed) describes readily aligned sites that are either simply present or absent. These sites tend to be occupied by high-mannose glycans. The second pattern (shifting) refers to sites embedded in regions of extreme local length variation and is characterized by shifts in terms of the relative position and local density of sequons; these sites tend to be populated by complex carbohydrates. HIV, with its extreme variation in number and precise location of sequons, does not have a net increase in the number of sites over time at the population level. Primate lentiviral lineages have host species-dependent levels of sequon shifting, with HIV-1 in humans the most extreme. HCV E1 and E2 proteins, despite evolving extremely rapidly through point mutation, show limited sequon variation, although two shifting sites were identified. Human influenza A hemagglutinin H3 HA1 is accumulating sequons over time, but this trend is not evident in any other avian or human influenza A serotypes.

Digital steganography: hiding data within data

Abstract: Digital steganography is the art of inconspicuously hiding data within data. Steganography's goal in general is to hide data well enough that unintended recipients do not suspect the steganographic medium of containing hidden data. The software and links mentioned in this article are just a sample of the steganography tools currently available. As privacy concerns continue to develop along with the digital communication domain, steganography will undoubtedly play a growing role in society. For this reason, it is important that we are aware of digital steganography technology and its implications. Equally important are the ethical concerns of using steganography and steganalysis. Steganography enhances rather than replaces encryption. Messages are not secure simply by virtue of being hidden. Likewise, steganography is not about keeping your message from being known - it's about keeping its existence from being known.