New Results on Standard Solar Models

We describe the current status of solar modelling and focus on the problems originated with the introduction of solar abundance determinations with low CNO abundance values. We use models computed with solar abundance compilations obtained during the last decade, including the newest published abundances by Asplund and collaborators. Results presented here make focus both on helioseismic properties and the models as well as in the neutrino fluxes predictions. We also discuss changes in radiative opacities to restore agreement between helioseismology, solar models, and solar abundances and show the effect of such modifications on solar neutrino fluxes.Comment: 9 pages. Review talk presented at "Synergies between solar and stellar modelling", Rome, June 2009. To be published by Astrophysics and Space Scienc

Heavy metal content of vegetables irrigated with mixtures of wastewater and sewage sludge in Zimbabwe: Implications for human health

There is growing public concern in Zimbabwe over the illegal cultivation of vegetables on soils amended with sewage sludge or irrigated with admixtures of sewage and sewage sludge. Excessive accumulation of heavy metals in agricultural soils may not only result in environmental contamination, but lead to elevated heavy metal uptake by crops, which may affect food quality and safety. The work reported here studied heavy metal concentrations in crops irrigated with sewage sludge and sewage/sewage sludge admixtures at Firle Municipal Farm in Harare. The crops analysed in this study are heavily contaminated with the four regulated elements Cd, Cu, Pb and Zn. This contamination is at its highest in two of the staple dietary crops maize and tsunga. Tsunga leaves contained 3.68 mg kg-1 Cd, over 18 times the permissible level by the EU standards (0.2 mg kg-1); Cu concentrations were 111 mg kg-1, 5 times the EU Standard (20 mg kg-1); concentrations of Pb were 6.77 mg kg-1, over 22 times the permissible levels allowed by both EU standards and UK guidelines (0.3 mg kg-1); Zn concentrations were 221 mg kg-1, over 4 times the guideline value (50 mg kg-1). The other plants (beans, maize, peppers and sugarcane) also contained concentrations of heavy metals above the permissible levels. Furthermore the concentrations observed in this study were higher than those reported by other workers who have examined vegetation from other contaminated sites. This study highlights the potential risks involved in the cultivation and consumption of vegetables on plots irrigated with sewage sludge, a practice which may place at risk the health of the urban population who consume these vegetables

YREC: The Yale Rotating Stellar Evolution Code

The stellar evolution code YREC is outlined with emphasis on its applications to helio- and asteroseismology. The procedure for calculating calibrated solar and stellar models is described. Other features of the code such as a non-local treatment of convective core overshoot, and the implementation of a parametrized description of turbulence in stellar models, are considered in some detail. The code has been extensively used for other astrophysical applications, some of which are briefly mentioned at the end of the paper.Comment: 10 pages, 2 figures, ApSS accepte

Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice.

Acknowledgements We are grateful to the University of Nottingham glasshouse staff for their assistance with general plant maintenance. We acknowledge the insight of two anonymous reviews whose comments greatly improved this manuscript. JR and JNF were supported by the Palaeobenchmarking Resilient Agriculture Systems (PalaeoRAS) project funded by the Future Food Beacon of the University of Nottingham.Peer reviewedPostprin

CLES, Code Liegeois d'Evolution Stellaire

Cles is an evolution code recently developed to produce stellar models meeting the specific requirements of studies in asteroseismology. It offers the users a lot of choices in the input physics they want in their models and its versatility allows them to tailor the code to their needs and implement easily new features. We describe the features implemented in the current version of the code and the techniques used to solve the equations of stellar structure and evolution. A brief account is given of the use of the program and of a solar calibration realized with it.Comment: Comments: 8 pages, Astrophys. Space Sci. CoRoT-ESTA Volume, in the pres

ASTEC -- the Aarhus STellar Evolution Code

The Aarhus code is the result of a long development, starting in 1974, and still ongoing. A novel feature is the integration of the computation of adiabatic oscillations for specified models as part of the code. It offers substantial flexibility in terms of microphysics and has been carefully tested for the computation of solar models. However, considerable development is still required in the treatment of nuclear reactions, diffusion and convective mixing.Comment: Astrophys. Space Sci, in the pres

Stellar evolution and modelling stars

In this chapter I give an overall description of the structure and evolution of stars of different masses, and review the main ingredients included in state-of-the-art calculations aiming at reproducing observational features. I give particular emphasis to processes where large uncertainties still exist as they have strong impact on stellar properties derived from large compilations of tracks and isochrones, and are therefore of fundamental importance in many fields of astrophysics.Comment: Lecture presented at the IVth Azores International Advanced School in Space Sciences on "Asteroseismology and Exoplanets: Listening to the Stars and Searching for New Worlds" (arXiv:1709.00645), which took place in Horta, Azores Islands, Portugal in July 201

Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano droplets. Solvation of hydrophobic and charged species change drastically in nano water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. Interaction between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types