First report of Rice stripe necrosis virus infecting rice in Sierra Leone

While Rice stripe necrosis virus (RSNV, Benyvirus, Benyviridae) has been reported on rice plants on two continents, little is known about the diversity of this multipartite virus which is transmitted by the plasmodiophorid protist Polymyxa graminis. First identified in 1983 in the Côte d´Ivoire (Fauquet & Thouvenel, 1983), the disease had previously been observed in Sierra Leone without formal identification of the causal agent (Buddenhagen, pers. comm.). Later, the virus was reported in South and Central America (Colombia, Ecuador, Panama and Brazil) causing up to 40% yield losses (Morales et al., 1999). Recently, RSNV was identified for the first time in several African countries including Burkina Faso (Sérémé et al., 2014), Benin (Oludare et al., 2015) and Mali (Decroës et al., 2017) suggesting a re-emergence of the virus in Africa.In 2019, symptoms of leaf-crinkling and stripe necrosis were observed on a rice plant from the Bo District in Sierra Leone (Fig. 1). Leaf samples were analysed by serological and molecular methods to confirm the presence of RSNV in Sierra Leone. RSNV was detected by plate-trapped antibody (PTA)- ELISA using a polyclonal antiserum against RSNV (Fauquet & Thouvenel, 1983).The presence of the virus was confirmed after total RNA extraction using 0.05 g of leaves and the RNeasy Plant Mini Kit (Qiagen) and RT-PCR amplification (10 U/μl M-MLV-reverse transcriptase, Promega; 10 U/μl Dynazyme, Finnzyme) as described previously (Sérémé et al., 2014, Oludare et al., 2015) with primers RSNV1-2901F 5′-TGAATTTGGTGCTCTCTTG-3′ / RSNV1-3827R 5′-TGTGGCGTTTCCAGACCTAAA-3´ and RSNV2-5´ 5´-TATCACTACTGACGAATTCCACCTAC-3´ / RSNV2-1223R 5´-AATCTGCGGCCTGTTTTGTA-3´. Specific amplicons, 926 and 1241 nt in length, were generated corresponding to sequences in the helicase domain and the coat protein (CP) genes on RSNV RNA 1 and RNA 2, respectively. The amplicons were sequenced directly and the sequences deposited in GenBank (Accession Nos. MN750254 and MN750255, respectively).The helicase sequence obtained from the Sierra Leone RSNV isolate showed 1.8-7.3% genetic distance with those from South America (EU099844.3, MG792544, MG792545, MG792546) and only 1.4-2.2% with those from Africa (KP099623, MF115599, MF115600, MF115601, MF115602, MF115603, MK170452, MK170453). The phylogenetic analysis based on the helicase domain included the sequence obtained from the Sierra Leone within a cluster represented by RSNV from South America and West Africa (Fig. 2a). In contrast, the CP sequence from the Sierra Leone RSNV isolate revealed an unexpected genetic differentiation as compared to all the other sequences from South America (5.6%; NC_038774) or Africa (5.2-6.5%; LK023710, MF115604, MF115605, MF115606, MF115607, MF115608, MK170454, MK170455). Interestingly, the CP sequence from Sierra Leone is located at a basal position in the phylogeny (Fig. 2b).To our knowledge, this is the first confirmed report of RSNV in Sierra Leone. Further studies are needed to assess the molecular and biological diversity of RSNV, the spatial distribution and the incidence of this re-emerging rice disease in Africa.Fil: Tucker, M. J.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Giovani Celli, Marcos Giovani. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Conteh, A. B.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Taylor, D. R.. Sierra Leone Agricultural Research Institute; Sierra LeonaFil: Hebrard, Andrés. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; FranciaFil: Poulicard, N.. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; Franci

Temperature effects on dislocation core energies in silicon and germanium

Temperature effects on the energetics of the 90-degree partial dislocation in silicon and germanium are investigated, using non-equilibrium methods to estimate free energies, coupled with Monte Carlo simulations. Atomic interactions are described by Tersoff and EDIP interatomic potentials. Our results indicate that the vibrational entropy has the effect of increasing the difference in free energy between the two possible reconstructions of the 90-degree partial, namely, the single-period and the double-period geometries. This effect further increases the energetic stability of the double-period reconstruction at high temperatures. The results also indicate that anharmonic effects may play an important role in determining the structural properties of these defects in the high-temperature regime.Comment: 8 pages in two-column physical-review format with six figure

Spirometry: A practical lifespan predictor of global health and chronic respiratory and non-respiratory diseases

Objectives. 1. To review and discuss available evidence supporting that spirometry is an overlooked global health marker, that could be used regularly through the lifespan to monitor human health and predict risk of chronic respiratory and other chronic non-communicable diseases (NCDs). 2. To discuss the challenges and opportunities that this proposal faces.Summary of key data. First, spirometry is essential to assess and monitor respiratory health. Second, spirometry adds prognostic value to other well-accepted health markers used in clinical practice, such as blood pressure, body mass index, glucose and blood lipids, by identifying individuals at risk, not only of respiratory diseases, but also of other NCDs, particularly cardiovascular and metabolic disorders. Conclusion. Although we acknowledge that research gaps still exist, we propose that spirometry assessed during childhood, adolescence and early and late adulthood can be a reproducible, non-invasive, safe and affordable global health marker to identify individuals in the general population at risk of respiratory and non-respiratory NCDs. In this context, spirometry may act as the caged canaries that miners used to carry into mines to alert them of dangerous accumulations of gases, thus providing an early warning and save lives

Atomic structure of dislocation kinks in silicon

We investigate the physics of the core reconstruction and associated structural excitations (reconstruction defects and kinks) of dislocations in silicon, using a linear-scaling density-matrix technique. The two predominant dislocations (the 90-degree and 30-degree partials) are examined, focusing for the 90-degree case on the single-period core reconstruction. In both cases, we observe strongly reconstructed bonds at the dislocation cores, as suggested in previous studies. As a consequence, relatively low formation energies and high migration barriers are generally associated with reconstructed (dangling-bond-free) kinks. Complexes formed of a kink plus a reconstruction defect are found to be strongly bound in the 30-degree partial, while the opposite is true in the case of 90-degree partial, where such complexes are found to be only marginally stable at zero temperature with very low dissociation barriers. For the 30-degree partial, our calculated formation energies and migration barriers of kinks are seen to compare favorably with experiment. Our results for the kink energies on the 90-degree partial are consistent with a recently proposed alternative double-period structure for the core of this dislocation.Comment: 12 pages, two-column style with 8 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#rn_di

Venous Admixture in COPD: Pathophysiology and Therapeutic Approaches

Chronic obstructive and interstitial lung diseases impair pulmonary gas exchange leading to wasted ventilation (alveolar dead space) and wasted perfusion (venous admixture). These two fundamental types of abnormality represent opposite ends of the spectrum of ventilation-perfusion mismatch with V˙/Q˙ ratios of infinity and zero. Treatment approaches that improve airway function, reduce air trapping and hyperinflation have received much attention and might be successful at ameliorating the problems associated with high V˙/Q˙. However, in patients with low V˙/Q˙ abnormality in whom venous admixture leads to hypoxemia, there are few therapeutic options. Indeed, some patients are refractory to treatment with supplemental oxygen particularly during exercise. Theoretically these patients could benefit from an intervention that increased mixed venous oxygen content thereby ameliorating the deleterious effects of venous admixture. In this perspective article we discuss the mechanisms whereby venous admixture contributes to hypoxemia and reduced oxygen delivery to tissues. We explore methods which could potentially increase mixed venous oxygen content thus ameliorating the deleterious effects of venous admixture. One such intervention that warrants further investigation is the therapeutic creation of an arterio-venous fistula. Such an approach would be novel, simple and minimally invasive. There is reason to believe that complications would be minor leading to a favorable risk-benefit analysis. This approach to treatment could have significant impact for patients with COPD but should also benefit any patient with chronic hypoxemia that impairs exercise performance

Stopping of Charged Particles in a Magnetized Classical Plasma

The analytical and numerical investigations of the energy loss rate of the test particle in a magnetized electron plasma are developed on the basis of the Vlasov-Poisson equations, and the main results are presented. The Larmor rotation of a test particle in a magnetic field is taken into account. The analysis is based on the assumption that the energy variation of the test particle is much less than its kinetic energy. The obtained general expression for stopping power is analyzed for three cases: (i) the particle moves through a collisionless plasma in a strong homogeneous magnetic field; (ii) the fast particle moves through a magnetized collisionless plasma along the magnetic field; and (iii) the particle moves through a magnetized collisional plasma across a magnetic field. Calculations are carried out for the arbitrary test particle velocities in the first case, and for fast particles in the second and third cases. It is shown that the rate at which a fast test particle loses energy while moving across a magnetic field may be much higher than the loss in the case of motion through plasma without magnetic field.Comment: 14 pages, 3 figures, LaTe

Surfaces roughness effects on the transmission of Gaussian beams by anisotropic parallel plates

Influence of the plate surfaces roughness in precise ellipsometry experiments is studied. The realistic case of a Gaussian laser beam crossing a uniaxial platelet is considered. Expression for the transmittance is determined using the first order perturbation theory. In this frame, it is shown that interference takes place between the specular transmitted beam and the scattered field. This effect is due to the angular distribution of the Gaussian beam and is of first order in the roughness over wavelength ratio. As an application, a numerical simulation of the effects of quartz roughness surfaces at normal incidence is provided. The interference term is found to be strongly connected to the random nature of the surface roughness.Comment: 18 pages, Journal of Physics D: Applied Physics, volume 36, issue 21, pages 2697 - 270

The Impact of HAART on the Respiratory Complications of HIV Infection: Longitudinal Trends in the MACS and WIHS Cohorts

Objective: To review the incidence of respiratory conditions and their effect on mortality in HIV-infected and uninfected individuals prior to and during the era of highly active antiretroviral therapy (HAART). Design: Two large observational cohorts of HIV-infected and HIV-uninfected men (Multicenter AIDS Cohort Study [MACS]) and women (Women's Interagency HIV Study [WIHS]), followed since 1984 and 1994, respectively. Methods: Adjusted odds or hazards ratios for incident respiratory infections or non-infectious respiratory diagnoses, respectively, in HIV-infected compared to HIV-uninfected individuals in both the pre-HAART (MACS only) and HAART eras; and adjusted Cox proportional hazard ratios for mortality in HIV-infected persons with lung disease during the HAART era. Results: Compared to HIV-uninfected participants, HIV-infected individuals had more incident respiratory infections both pre-HAART (MACS, odds ratio [adjusted-OR], 2.4; 95% confidence interval [CI], 2.2-2.7; p<0.001) and after HAART availability (MACS, adjusted-OR, 1.5; 95%CI 1.3-1.7; p<0.001; WIHS adjusted-OR, 2.2; 95%CI 1.8-2.7; p<0.001). Chronic obstructive pulmonary disease was more common in MACS HIV-infected vs. HIV-uninfected participants pre-HAART (hazard ratio [adjusted-HR] 2.9; 95%CI, 1.02-8.4; p = 0.046). After HAART availability, non-infectious lung diseases were not significantly more common in HIV-infected participants in either MACS or WIHS participants. HIV-infected participants in the HAART era with respiratory infections had an increased risk of death compared to those without infections (MACS adjusted-HR, 1.5; 95%CI, 1.3-1.7; p<0.001; WIHS adjusted-HR, 1.9; 95%CI, 1.5-2.4; p<0.001). Conclusion: HIV infection remained a significant risk for infectious respiratory diseases after the introduction of HAART, and infectious respiratory diseases were associated with an increased risk of mortality. © 2013 Gingo et al