Viral Resistance in Hepatitis B: Prevalence and Management

Hepatitis B is a DNA virus affecting hundreds of millions of individuals worldwide. As the clinical sequelae of cirrhosis and hepatocellular cancer are increasingly recognized to be related to viral levels, the impetus increases to offer treatment to those previously not treated. With the development of more robust antivirals with reasonable safety profiles, long-term treatment is becoming more common. The oral nucleos(t)ide analogs have become the preferred first-line therapies for most genotypes of hepatitis B. Five are now available, all with different potencies and resistance profiles. Long-term data spanning several years are now available for most compounds in this arena. This article focuses on the common natural variants and those secondary to nucleos(t)ide therapy, as well as diagnostic methods to detect resistance

Consonance perception beyond the traditional existence region of pitch

Some theories posit that the perception of consonance is based on neural periodicity detection, which is dependent on accurate phase locking of auditory nerve fibers to features of the stimulus waveform. In the current study, 15 listeners were asked to rate the pleasantness of complex tone dyads (2 note chords) forming various harmonic intervals and bandpass filtered in a high-frequency region (all components >5.8 kHz), where phase locking to the rapid stimulus fine structure is thought to be severely degraded or absent. The two notes were presented to opposite ears. Consonant intervals (minor third and perfect fifth) received higher ratings than dissonant intervals (minor second and tritone). The results could not be explained in terms of phase locking to the slower waveform envelope because the preference for consonant intervals was higher when the stimuli were harmonic, compared to a condition in which they were made inharmonic by shifting their component frequencies by a constant offset, so as to preserve their envelope periodicity. Overall the results indicate that, if phase locking is indeed absent at frequencies greater than ∼5 kHz, neural periodicity detection is not necessary for the perception of consonance

Stage-Specific Inhibition of MHC Class I Presentation by the Epstein-Barr Virus BNLF2a Protein during Virus Lytic Cycle

gamma-herpesvirus Epstein-Barr virus (EBV) persists for life in infected individuals despite the presence of a strong immune response. During the lytic cycle of EBV many viral proteins are expressed, potentially allowing virally infected cells to be recognized and eliminated by CD8+ T cells. We have recently identified an immune evasion protein encoded by EBV, BNLF2a, which is expressed in early phase lytic replication and inhibits peptide- and ATP-binding functions of the transporter associated with antigen processing. Ectopic expression of BNLF2a causes decreased surface MHC class I expression and inhibits the presentation of indicator antigens to CD8+ T cells. Here we sought to examine the influence of BNLF2a when expressed naturally during EBV lytic replication. We generated a BNLF2a-deleted recombinant EBV (ΔBNLF2a) and compared the ability of ΔBNLF2a and wild-type EBV-transformed B cell lines to be recognized by CD8+ T cell clones specific for EBV-encoded immediate early, early and late lytic antigens. Epitopes derived from immediate early and early expressed proteins were better recognized when presented by ΔBNLF2a transformed cells compared to wild-type virus transformants. However, recognition of late antigens by CD8+ T cells remained equally poor when presented by both wild-type and ΔBNLF2a cell targets. Analysis of BNLF2a and target protein expression kinetics showed that although BNLF2a is expressed during early phase replication, it is expressed at a time when there is an upregulation of immediate early proteins and initiation of early protein synthesis. Interestingly, BNLF2a protein expression was found to be lost by late lytic cycle yet ΔBNLF2a-transformed cells in late stage replication downregulated surface MHC class I to a similar extent as wild-type EBV-transformed cells. These data show that BNLF2a-mediated expression is stage-specific, affecting presentation of immediate early and early proteins, and that other evasion mechanisms operate later in the lytic cycle

Disinfection of football protective equipment using chlorine dioxide produced by the ICA TriNova system

<p>Abstract</p> <p>Backround</p> <p>Community-associated methicillin-resistant <it>Staphylococcus aureus </it>outbreaks have occurred in individuals engaged in athletic activities such as wrestling and football. Potential disease reduction interventions include the reduction or elimination of bacteria on common use items such as equipment. Chlorine dioxide has a long history of use as a disinfectant. The purpose of this investigation was to evaluate the ability of novel portable chlorine dioxide generation devices to eliminate bacteria contamination of helmets and pads used by individuals engaged in football.</p> <p>Methods</p> <p>In field studies, the number of bacteria associated with heavily used football helmets and shoulder pads was determined before and after overnight treatment with chlorine dioxide gas. Bacteria were recovered using cotton swabs and plated onto trypticase soy agar plates. In laboratory studies, <it>Staphylococcus aureus </it>was applied directly to pads. The penetration of bacteria into the pads was determined by inoculating agar plates with portions of the pads taken from the different layers of padding. The ability to eliminate bacteria on the pad surface and underlying foam layers after treatment with chlorine dioxide was also determined.</p> <p>Results</p> <p>Rates of recovery of bacteria after treatment clearly demonstrated that chlorine dioxide significantly (p < 0.001) reduce and eliminated bacteria found on the surface of pads. For example, the soft surface of shoulder pads from a university averaged 2.7 × 10³recoverable bacteria colonies before chlorine dioxide treatment and 1.3 × 10²recoverable colonies after treatment. In addition, the gas was capable of penetrating the mesh surface layer and killing bacteria in the underlying foam pad layers. Here, 7 × 10³to 4.5 × 10³laboratory applied <it>S. aureus </it>colonies were recovered from underlying layers before treatment and 0 colonies were present after treatment. Both naturally occurring bacteria and <it>S. aureus </it>were susceptible to the treatment process.</p> <p>Conclusion</p> <p>Results of this study have shown that chlorine dioxide can easily and safely be used to eliminate bacteria contamination of protective pads used by football players. This could serve to reduce exposure to potential pathogens such as the methicillin-resistant <it>Staphylococcus aureus </it>among this group of individuals.</p

Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other. Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the availability of both direct and reverse mixed sequences of the same template. We describe a simple yet accurate method, which uses dynamic programming optimization to predict superimposed allelic sequences solely from a string of letters representing peaks within an individual mixed trace. We used the method to decode 104 human traces (mean length 294 bp) containing heterozygous indels 5 to 30 bp with a mean of 99.1% bases per allelic sequence reconstructed correctly and unambiguously. Simulations with artificial sequences have demonstrated that the method yields accurate reconstructions when (1) the allelic sequences forming the mixed trace are sufficiently similar, (2) the analyzed fragment is significantly longer than the indel, and (3) multiple indels, if present, are well-spaced. Because these conditions occur in most encountered DNA sequences, the method is widely applicable. It is available as a free Web application Indelligent at http://ctap.inhs.uiuc.edu/dmitriev/indel.asp

Unsuccessful therapy with adefovir and entecavir-tenofovir in a patient with chronic hepatitis B infection with previous resistance to lamivudine: a fourteen-year evolution of hepatitis B virus mutations

<p>Abstract</p> <p>Background</p> <p>Complex mutants can be selected under sequential selective pressure by HBV therapy. To determine hepatitis B virus genomic evolution during antiviral therapy we characterized the HBV quasi-species in a patient who did no respond to therapy following lamivudine breakthrough for a period of 14 years.</p> <p>Case Presentation</p> <p>The polymerase and precore/core genes were amplified and sequenced at determined intervals in a period of 14 years. HBV viral load and HBeAg/Anti-HBe serological profiles as well as amino transferase levels were also measured. A mixture of lamivudine-resistant genotype A2 HBV strains harboring the rtM204V mutation coexisted in the patient following viral breakthrough to lamivudine. The L180M+M204V dominant mutant displayed strong lamivudine-resistance. As therapy was changed to adefovir, then to entecavir, and finally to entecavir-tenofovir the viral load showed fluctuations but lamivudine-resistant strains continued to be selected, with minor contributions to the HBV quasi-species composition of additional resistance-associated mutations. At the end of the 14-year follow up period, high viral loads were predominant, with viral strains harboring the lamivudine-resistance signature rtL180M+M204V. The precore/core frame A1762T and G1764A double mutation was detected before treatment and remaining in this condition during the entire follow-up. Specific entecavir and tenofovir primary resistance-associated mutations were not detected at any time. Plasma concentrations of tenofovir indicated adequate metabolism of the drug.</p> <p>Conclusions</p> <p>We report the selection of HBV mutants carrying well-defined primary resistance mutations that escaped lamivudine in a fourteen-year follow-up period. With the exception of tenofovir resistance mutations, subsequent unselected primary resistance mutations were detected as minor populations into the HBV quasispecies composition during adefovir or entecavir monotherapies. Although tenofovir is considered an appropriate therapeutic alternative for the treatment of entecavir-unresponsive patients, its use was not effective in the case reported here.</p

Rheological Characteristics of Municipal Thickened Excess Activated Sludge (TEAS): Impacts of pH, Temperature, Solid Concentration and Polymer Dose

Rheological characterization of sludge is known to be an essential tool to optimize flow, mixing and other process parameters in wastewater treatment plants. This study deals with the characterization of thickened excess activated sludge in comparison to raw primary sludge and excess activated sludge. The effects of key parameters (total solid concentration, temperature, and pH) on the rheology and flow behavior of thickened excess activated sludge were studied. The rheological investigations were carried out for total solid concentration range of 0.9–3.7 %w/w, temperature range of 23–55 °C, and pH range of 3.6–10.0. Different rheological model equations were fitted to the experimental data. The model equations with better fitting were used to calculate the yield stress, apparent, zero-rate, infinite-rate viscosities, flow consistency index, and flow index. The decrease in concentration from 3.7 to 3.1 %w/w resulted in a drastic reduction of yield stress from 27.6 to 11.0 Pa, while a further reduction of yield stress to 1.3 Pa was observed as solid concentration was reduced to 1.3 %w/w. The viscosity at higher shear rate (>600 s−1) decreased from 0.05 Pa·s down to 0.008 Pa·s when the total solid concentration was reduced from 3.7 to 0.9 %. Yield stress decreased from 20.1 Pa down to 8.3 Pa for the Bingham plastic model when the temperature was raised from 25 to 55 °C. Activation energy and viscosity also showed decreasing trends with increasing temperature. Yield stress of thickened excess activated sludge increased from a value of 6.0 Pa to 8.3 Pa when the pH was increased from 3.6 to 10.0. The effect of polymer dose on the rheological behavior of the thickening of excess activated sludge was also investigated, and the optimum polymer dosage for enhanced thickener performance was determined to be 1.3 kg/ton DS

Genome Majority Vote Improves Gene Predictions

Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps

Mapping the fragmentation of acetylene with femtosecond resolution pump probe at LCLS using 2, 3, and 4 particle coincidences.

A three-layer delay line anode detector has been used in x-ray pump x-ray probe time-resolved measurement at LCLS. We used ~10 fs long pulses to initiate and probe ultrafast dynamics in the dication of acetylene. The dynamics are discerned from the temporal evolution of multi-particle coincidences

Perception of isolated chords: Examining frequency of occurrence, instrumental timbre, acoustic descriptors and musical training

This study investigated the perception of isolated chords using a combination of experimental manipulation and exploratory analysis. Twelve types of chord (five triads and seven tetrads) were presented in two instrumental timbres (piano and organ) to listeners who rated the chords for consonance, pleasantness, stability and relaxation. Listener ratings varied by chord, by timbre, and according to musical expertise, and revealed that musicians distinguished consonance from the other variables in a way that other listeners did not. To further explain the data, a principal component analysis and linear regression examined three potential predictors of the listener ratings. First, each chord’s frequency of occurrence was obtained by counting its appearances in selected works of music. Second, listeners rated their familiarity with the instrumental timbre in which the chord was played. Third, chords were described using a set of acoustic features derived using the Timbre Toolbox and MIR Toolbox. Results of the study indicated that listeners’ ratings of both consonance and stability were influenced by the degree of musical training and knowledge of tonal hierarchy. Listeners’ ratings of pleasantness and relaxation, on the other hand, depended more on the instrumental timbre and other acoustic descriptions of the chord