Relativistic Mean Field Calculations of Λ\Lambda and Σ\Sigma Hypernuclei

Single--particle spectra of $\Lambda$ and $\Sigma$ hypernuclei are calculated within a relativistic mean--field theory. The hyperon couplings used are compatible with the $\Lambda$ binding in saturated nuclear matter, neutron-star masses and experimental data on $\Lambda$ levels in hypernuclei. Special attention is devoted to the spin-orbit potential for the hyperons and the influence of the $\rho$-meson field (isospin dependent interaction).Comment: 18 pages, including 2 figs., figs. 1 and 4-6 available as postscript-datasets on request; written in Latex, report# LBL-3303

Impurity-enhanced Aharonov-Bohm effect in neutral quantum-ring magnetoexcitons

We study the role of impurity scattering on the photoluminescence (PL) emission of polarized magnetoexcitons. We consider systems where both the electron and hole are confined on a ring structure (quantum rings) as well as on a type-II quantum dot. Despite their neutral character, excitons exhibit strong modulation of energy and oscillator strength in the presence of magnetic fields. Scattering impurities enhance the PL intensity on otherwise "dark" magnetic field windows and non-zero PL emission appears for a wide magnetic field range even at zero temperature. For higher temperatures, impurity-induced anticrossings on the excitonic spectrum lead to unexpected peaks and valleys on the PL intensity as function of magnetic field. Such behavior is absent on ideal systems and can account for prominent features in recent experimental results.Comment: 7 pages, 7 figures, RevTe

A strategy to combine pathway-targeted low toxicity drugs in ovarian cancer.

Serous Ovarian Cancers (SOC) are frequently resistant to programmed cell death. However, here we describe that these programmed death-resistant cells are nonetheless sensitive to agents that modulate autophagy. Cytotoxicity is not dependent upon apoptosis, necroptosis, or autophagy resolution. A screen of NCBI yielded more than one dozen FDA-approved agents displaying perturbed autophagy in ovarian cancer. The effects were maximized via combinatorial use of the agents that impinged upon distinct points of autophagy regulation. Autophagosome formation correlated with efficacy in vitro and the most cytotoxic two agents gave similar effects to a pentadrug combination that impinged upon five distinct modulators of autophagy. However, in a complex in vivo SOC system, the pentadrug combination outperformed the best two, leaving trace or no disease and with no evidence of systemic toxicity. Targeting the autophagy pathway in a multi-modal fashion might therefore offer a clinical option for treating recalcitrant SOC

Coulomb interaction effects on the electronic structure of radial polarized excitons in nanorings

The electronic structure of radially polarized excitons in structured nanorings is analyzed, with emphasis in the ground-state properties and their dependence under applied magnetic fields perpendicular to the ring plane. The electron-hole Coulomb attraction has been treated rigorously, through numerical diagonalization of the full exciton Hamiltonian in the non-interacting electron-hole pairs basis. Depending on the relative weight of the kinetic energy and Coulomb contributions, the ground-state of polarized excitons has "extended" or "localized" features. In the first case, corresponding to small rings dominated by the kinetic energy, the ground-state shows Aharonov-Bohm (AB) oscillations due to the individual orbits of the building particles of the exciton. In the localized regime, corresponding to large rings dominated by the Coulomb interaction, the only remaining AB oscillations are due to the magnetic flux trapped between the electron and hole orbits. This dependence of the exciton, a neutral excitation, on the flux difference confirms this feature as a signature of Coulomb dominated polarized excitons. Analytical approximations are provided in both regimens, which accurate reproduce the numerical results.Comment: 9 pages, including 6 figure

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe ‘equivalog’ families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at and

Red giant bound on the axion-electron coupling reexamined

If axions or other low-mass pseudoscalars couple to electrons (``fine structure constant'' $\alpha_a$) they are emitted from red giant stars by the Compton process $\gamma+e\to e+a$ and by bremsstrahlung $e+(Z,A)\to (Z,A)+e+a$. We construct a simple analytic expression for the energy-loss rate for all conditions relevant for a red giant and include axion losses in evolutionary calculations from the main sequence to the helium flash. We find that \alpha_a\lapprox0.5\mn(-26) or m_a\lapprox 9\,\meV/\cos^2\beta lest the red giant core at helium ignition exceed its standard mass by more than 0.025\,\MM_\odot, in conflict with observational evidence. Our bound is the most restrictive limit on $\alpha_a$, but it does not exclude the possibility that axion emission contributes significantly to the cooling of ZZ~Ceti stars such as G117--B15A for which the period decrease was recently measured.Comment: 11 pages, uuencoded and compressed postscript fil

Detection of putative new mutacins by bioinformatic analysis using available web tools

In order to characterise new bacteriocins produced by Streptococcus mutans we perform a complete bioinformatic analyses by scanning the genome sequence of strains UA159 and NN2025. By searching in the adjacent genomic context of the two-component signal transduction system we predicted the existence of many putative new bacteriocins' maturation pathways and some of them were only exclusive to a group of Streptococcus. Computational genomic and proteomic analysis combined to predictive functionnal analysis represent an alternative way for rapid identification of new putative bacteriocins as well as new potential antimicrobial drugs compared to the more traditional methods of drugs discovery using antagonism tests