A complete ancient RNA genome : identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus

The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes

Oscillator strengths and line widths of dipole-allowed transitions in ¹⁴N₂ between 89.7 and 93.5 nm

Line oscillator strengths in the 20 electric dipole-allowed bands of ¹⁴N₂ in the 89.7–93.5nm (111480–106950cm⁻¹) region are reported from photoabsorptionmeasurements at an instrumental resolution of ∼6mÅ (0.7cm⁻¹) full width at half maximum. The absorptionspectrum comprises transitions to vibrational levels of the 3pσᵤc′₄¹Σᵤ⁺, 3pπᵤc³Πᵤ, and 3sσgo₃¹ΠᵤRydberg states and of the b′¹Σᵤ⁺ and b¹Πᵤ valence states. The J dependences of band f values derived from the experimental line f values are reported as polynomials in J′(J′+1) and are extrapolated to J′=0 in order to facilitate comparisons with results of coupled Schrödinger-equation calculations. Most bands in this study are characterized by a strong J dependence of the band f values and display anomalous P-, Q-, and R-branch intensity patterns. Predissociation line widths, which are reported for 11 bands, also exhibit strong J dependences. The f value and line width patterns can inform current efforts to develop comprehensive spectroscopic models that incorporate rotational effects and predissociation mechanisms, and they are critical for the construction of realistic atmospheric radiative-transfer models.This work was supported in part by NASA Grant No. NNG05GA03G to Wellesley College and Australian Research Council Discovery Program Grant No. DP0558962

ADULT NEST ATTENDANCE AND DIET OF NESTLING RESPLENDENT QUETZALS (PHAROMACHRUS MOCINNO) IN THE TALAMANCA MOUNTAINS OF SOUTHERN COSTA RICA

Abstract ∙ Resplendent Quetzals (Pharomachrus mocinno) inhabit mid to high elevation forests from southern Mexico to Panama. Lipid rich fruits from the Lauraceae family have been found to account for a large proportion of adult diet across their annual life cycle. To better understand the relationship between quetzals and Lauraceae during the breeding season, we studied food deliveries to nestlings in the Talamanca Mountains at San Gerardo de Dota, Costa Rica in the Rio Savegre watershed. Our study had four primary objectives: 1) determine parental contribution of males and females feeding nestling quetzals, 2) determine type of food delivered to nestling quetzals, 3) determine if deliveries of fruit items were related to their abundance and/or nutritional content and 4) determine if Lauraceae fruits made up a large proportion of nestling diets based on the high preference quetzals have displayed for fruits from this plant family. Hourly delivery rates were similar for the male and female (1.24 ± 0.68 and 1.44 ± 0.84). During the first 6 days, the largest proportion of the diet was animal prey; primarily lizards and beetles. After day 6, fruit rapidly became the dominant food item delivered to nestlings until fledging. The dominant number of fruits delivered to nestling quetzals were fruits from the Lauraceae family and included Ocotea holdrigeiana, Necatandra cufodontisii, and Aiouea costaricensis. All three had some of the highest protein and lipid content of all fruits delivered to nestlings. O. holdrigeiana had the highest protein and lipid content of all fruits delivered, had the lowest relative abundance, and was delivered more frequently than all other fruits. Conservation strategies for this species should take into account not just increasing available habitat, but also increasing habitat quality by focusing on species composition to provide abundant food plants for the Resplendent Quetzal to forage.Resumen ∙ Atención al nido y dieta de pichones del Quetzal Resplandeciente (Pharomachrus mocinno) en las Montañas Talamanca del sur de Costa Rica El Quetzal Resplandeciente (Pharomachrus mocinno) habita bosques de media a alta elevación del sur de México a Panamá. Frutas ricas en lípidos de la familia Lauraceae han sido consideradas constituyentes importantes de su dieta a lo largo de su ciclo anual de vida. Para entender mejor la relación entre quetzales y Lauraceae durante la temporada de cría, estudiamos entregas alimenticias a pichones en las montañas Talamanca en San Gerardo de Dota, Costa Rica en la Cuenca del Rio Savegre. Nuestro estudio tuvo cuatro objetivos primarios: 1) determinar la contribución del macho y la hembra en la alimentación de crías de quetzal, 2) determinar el tipo de entregas alimenticias a crías de quetzal, 3) determinar si las entregas de artículos frutales fueron relacionadas a su abundancia y/o contenido nutricional, y 4) determinar si frutas de Lauraceae conformaron una gran proporción de la dieta de crías de quetzal basado en la alta preferencia que quetzales han demostrado por frutas de esta familia. La proporción de entregas por hora fue similar en machos y hembras (1.24 ± 0.68 y 1.44 ± 0.84). Durante los primeros 6 días, presa animales constituyeron la mayor proporción de la dieta, ante todo lagartijas y escarabajos. Después del día 6, frutos constituyeron rápidamente el artículo de dieta dominante entregado a crías hasta que estas dejaron el nido. La mayor cantidad de frutas entregadas a crías de quetzal perteneció a la familia Lauraceae incluyendo Ocotea holdrigeiana, Nectandra cufodontisii, y Aiouea costaricensis. Las tres tuvieron el más alto contenido lipídico y de proteína de todas las frutas entregadas a crías. Interesantemente, O. holdrigeiana tuvo el más alto contenido lípido y de proteína de todas las frutas entregadas, la más baja abundancia relativa en el ambiente circundante, y fue utilizada más frecuentemente que todas las otras frutas. Estrategias de conservación para esta especie deben tomar en cuenta no solo incrementar el hábitat disponible, pero también incrementar la calidad del hábitat enfocándose en la composición de las especies vegetales, para asegurarse de proveer frutos en abundancia para la alimentación del Quetzal Resplandeciente

Survival probabilities in the double trapping reaction A +B -> B, B + C -> C

We consider the double trapping reaction A + B -> B, B + C -> C in one dimension. The survival probability of a given A particle is calculated under various conditions on the diffusion constants of the reactants, and on the ratio of initial B and C particle densities. The results are of more general form than those obtained in previous work on the problem.Comment: 5 page

Impact of patient selection and study characteristics on signal detection in placebo-controlled trials with antidepressants.

AbstractAn increasing rate of antidepressant trials fail due to large placebo responses. This analysis aimed to identify variables influencing signal detection in clinical trials of major depressive disorder. Patient-level data of randomized patients with a duloxetine dose ≥60 mg/day were obtained from Lilly. Total scores of the Hamilton Depression Rating scale (HAM-D) were used as efficacy endpoints. In total, 4661 patients from 14 studies were included in the analysis. The overall effect size (ES), based on the HAM-D total score at endpoint, between duloxetine and placebo was −0.272. Although no statistically significant interactions were found, the following results for factors influencing ES were seen: a very low ES (−0.157) in patients in the lowest baseline HAM-D category and in patients recruited in the last category of the recruitment period (−0.122). A higher ES in patients recruited in centers with a site-size at but not more than 2.5 times the average site-size for the study (−0.345). Study characteristics that resulted in low signal detection in our database were: 5 points, a high variability of placebo response (SD > 7 points HAM-D), >6 post baseline visits per study, and use of an active control drug. Simpler trial designs, more homogeneous and mid-sized study sites, a primary analysis based on a higher cutoff blinded to investigators to avoid the influence of score inflation in mild patients and, if possible, studies without an active control group could lead to a better signal detection of antidepressive efficacy

Sedation for Gastrointestinal Endoscopic Procedures in the Elderly: Getting Safer but Still Not Nearly Safe Enough

Previously published UK reports showed that excessively large doses of benzodiazepines and opiates were being commonly used to sedate elderly patients for gastrointestinal (GI) endoscopy. This unsafe practice has lead to avoidable morbidity and mortality. We have taken the opportunity provided by recent reports to examine whether GI endoscopy sedation practice in the elderly has improved in the light of this evidence and the publication of guidelines in which specific recommendations on sedation dosage are given

Attitudes Toward Breast Cancer Genetic Testing in Five Special Population Groups

Purpose: This study examined interest in and attitudes toward genetic testing in 5 different population groups. Methods: The survey included African American, Asian American, Latina, Native American, and Appalachian women with varying familial histories of breast cancer. A total of 49 women were interviewed in person. Descriptive and nonparametric statistical techniques were used to assess ethnic group differences. Results: Overall, interest in testing was high. All groups endorsed more benefits than risks. There were group differences regarding endorsement of specific benefits and risks: testing to “follow doctor recommendations” (p=0.017), “concern for effects on family” (p=0.044), “distrust of modern medicine” (p=0.036), “cost” (p=0.025), and “concerns about communication of results to others” (p=0.032). There was a significant inverse relationship between interest and genetic testing cost (p Conclusion: Cost may be an important barrier to obtaining genetic testing services, and participants would benefit by genetic counseling that incorporates the unique cultural values and beliefs of each group to create an individualized, culturally competent program. Further research about attitudes toward genetic testing is needed among Asian Americans, Native Americans, and Appalachians for whom data are severely lacking. Future study of the different Latina perceptions toward genetic testing are encouraged

New F-19 NMR methodology reveals structures of molecules in complex mixtures of fluorinated compounds

Although the number of natural fluorinated compounds is very small, fluorinated pharmaceuticals and agrochemicals are numerous. (19)F NMR spectroscopy has a great potential for the structure elucidation of fluorinated organic molecules, starting with their production by chemical or chemoenzymatic reactions, through monitoring their structural integrity, to their biotic and abiotic transformation and ultimate degradation in the environment. Additionally, choosing to incorporate (19)F into any organic molecule opens a convenient route to study reaction mechanisms and kinetics. Addressing limitations of the existing (19)F NMR techniques, we have developed methodology that uses (19)F as a powerful spectroscopic spy to study mixtures of fluorinated molecules. The proposed (19)F-centred NMR analysis utilises the substantial resolution and sensitivity of (19)F to obtain a large number of NMR parameters, which enable structure determination of fluorinated compounds without the need for their separation or the use of standards. Here we illustrate the (19)F-centred structure determination process and demonstrate its power by successfully elucidating the structures of chloramination disinfectant by-products of a single mono-fluorinated phenolic compound, which would have been impossible otherwise. This novel NMR approach for the structure elucidation of molecules in complex mixtures represents a major contribution towards the analysis of chemical and biological processes involving fluorinated compounds

Modelling extreme concentration from a source in a turbulent flow over rough wall

The concentration fluctuations in passive plumes from an elevated and a groundlevel source in a turbulent boundary layer over a rough wall were studied using large eddy simulation and wind tunnel experiment. The predictions of statistics up to second order moments were thereby validated. In addition, the trend of relative fluctuations far downstream for a ground level source was estimated using dimensional analysis. The techniques of extreme value theory were then applied to predict extreme concentrations by modelling the upper tail of the probability density function of the concentration time series by the Generalised Pareto Distribution. Data obtained from both the simulations and experiments were analysed in this manner. The predicted maximum concentration (?0) normalized by the local mean concentration (Cm) or by the local r.m.s of concentration fluctuation (crms), was extensively investigated. Values for ?0/Cm and ?0/crms as large as 50 and 20 respectively were found for the elevated source and 10 and 15 respectively for the ground-level source