Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide

A meta-analysis of long-term effects of conservation agriculture on maize grain yield under rain-fed conditions

Conservation agriculture involves reduced tillage, permanent soil cover and crop rotations to enhance soil fertility and to supply food from a dwindling land resource. Recently, conservation agriculture has been promoted in Southern Africa, mainly for maize-based farming systems. However, maize yields under rain-fed conditions are often variable. There is therefore a need to identify factors that influence crop yield under conservation agriculture and rain-fed conditions. Here, we studied maize grain yield data from experiments lasting 5 years and more under rain-fed conditions. We assessed the effect of long-term tillage and residue retention on maize grain yield under contrasting soil textures, nitrogen input and climate. Yield variability was measured by stability analysis. Our results show an increase in maize yield over time with conservation agriculture practices that include rotation and high input use in low rainfall areas. But we observed no difference in system stability under those conditions. We observed a strong relationship between maize grain yield and annual rainfall. Our meta-analysis gave the following findings: (1) 92% of the data show that mulch cover in high rainfall areas leads to lower yields due to waterlogging; (2) 85% of data show that soil texture is important in the temporal development of conservation agriculture effects, improved yields are likely on well-drained soils; (3) 73% of the data show that conservation agriculture practices require high inputs especially N for improved yield; (4) 63% of data show that increased yields are obtained with rotation but calculations often do not include the variations in rainfall within and between seasons; (5) 56% of the data show that reduced tillage with no mulch cover leads to lower yields in semi-arid areas; and (6) when adequate fertiliser is available, rainfall is the most important determinant of yield in southern Africa. It is clear from our results that conservation agriculture needs to be targeted and adapted to specific biophysical conditions for improved impact

Echocardiographic assessment of mitral valve morphology after Percutaneous Transvenous Mitral Commissurotomy (PTMC)

<p>Abstract</p> <p>Aims</p> <p>PTMC produces significant changes in mitral valve morphology as improvement in leaflets mobility. The determinants of such improvement have not been assessed before.</p> <p>Methods and results</p> <p>The study included 291 symptomatic patients with mitral stenosis undergoing PTMC. Post-PTMC subvalvular splitting area was a determinant of post-PTMC excursion in both the anterior (B 0.16, 95% CI 0.03 to 0.30, p < 0.05) and the posterior (B 0.12, 95% CI 0.01 to 0.24, p < 0.05) leaflets. Another determinant was the post-PTMC transmitral pressure gradient for anterior (B -0.02, 95% CI -0.04 to -0.005, p < 0.01) and posterior (B -0.01, 95% CI -0.04 to -0.005, p < 0.05) leaflets excursion. The relationship between post-PTMC MVA and leaflet excursion was non-linear "S curve". There was a steep increase of both anterior (p, 0.02) and posterior (p, 0.03) leaflets excursion with increased MVA till the MVA reached a value of about 1.5 cm²; after which both linear and S curves became nearly parallel.</p> <p>Conclusion</p> <p>The improvement in leaflets excursion after PTMC is determined by several morphologic and hemodynamic changes produced in the valve. The increase in MVA improves mobility within limit; after which any further increase in MVA is not associated by a significant improvement in mobility in both leaflets.</p

Prognostic Value of FDG-PET in Patients with Oropharyngeal Carcinoma Treated with Concurrent Chemoradiotherapy

Purpose: The purpose of this study was to evaluate the predictive value of 2-deoxy-2-[F-18] fluoro-D-glucose-positron emission tomography (FDG-PET) following concurrent chemoradiotherapy (CRT) on survival in patients with carcinoma of the oropharynx (OPC). Methods: Eighteen patients with primary OPC who underwent PET pre- and post-CRT were evaluated prospectively for survival. The prognostic performance of post-CRT PET and CT for recurrence was compared. Results: Patients with positive post-CRT PET exhibited significantly lower 2-year cause-specific survival and disease-free survival (50 % vs. 91%, PG0.05 and 0 % vs. 83%, PG0.0001); however, patients with positive post-CRT CT did not exhibit any significant difference (67 % vs. 83%, P= 0.416 and 50 % vs. 75%, P=0.070). Other factors, such as clinical and pre-CRT PET variables, also did not indicate any significant difference. The accuracy of prediction of residual and local recurrence for post-CRT PET and CT (local%/regional%) was 83%/94 % and 83%/78%, respectively. Conclusion: OPC patients with positive post-CRT PET exhibit poor survival. The prognostic accuracy of post-CRT PET is superior to that of CT. The results of post-CRT FDG-PET should be included in the management of the OPC patients

Knowledge, attitude and practice of women in Campinas, São Paulo, Brazil with respect to physical exercise in pregnancy: a descriptive study

<p>Abstract</p> <p>Background</p> <p>Pregnancy is a good time to develop healthy lifestyle habits including regular exercise and good nutrition. Programs of physical exercise for pregnant women have been recommended; however, there are few references on this subject in the literature. The objective of this study was to evaluate the knowledge, attitude and practice of pregnant women with respect to appropriate physical exercise during pregnancy, and also to investigate why some women do not exercise during pregnancy.</p> <p>Methods</p> <p>A descriptive study was conducted in which 161 women of 18 to 45 years of age were interviewed in the third trimester of pregnancy. These women were receiving prenatal care at National Health Service (SUS) primary healthcare units and had no pathologies for which physical exercise would constitute a risk. The women were selected at an ultrasonography clinic accredited to the SUS in Campinas, São Paulo. A previously elaborated knowledge, attitude and practice (KAP) questionnaire was used to collect data, which were then stored in an Epinfo database. Statistical analysis was conducted using Pearson's chi-square test and Fisher's exact test to evaluate the association between the study variables (p < 0.05).</p> <p>Results</p> <p>Almost two-thirds (65.6%) of the women were sufficiently informed about the practice of physical exercise during pregnancy and the vast majority (93.8%) was in favor of it. Nevertheless, only just over 20% of the women in this sample exercised adequately. Significant associations were found between an adequate knowledge of physical exercise during pregnancy and education level (p = 0.0014) and between the adequate practice of physical exercise during pregnancy and having had fewer pregnancies (p = 0.0001). Lack of time and feeling tired and uncomfortable were the principal reasons given by the women for not exercising.</p> <p>Conclusion</p> <p>These results suggest that women's knowledge concerning the practice of physical exercise during pregnancy is reasonable and their attitude is favorable; however, relatively few actually exercise during pregnancy.</p