Sequential stopping for high-throughput experiments

In high-throughput experiments, the sample size is typically chosen informally. Most formal sample-size calculations depend critically on prior knowledge. We propose a sequential strategy that, by updating knowledge when new data are available, depends less critically on prior assumptions. Experiments are stopped or continued based on the potential benefits in obtaining additional data. The underlying decision-theoretic framework guarantees the design to proceed in a coherent fashion. We propose intuitively appealing, easy-to-implement utility functions. As in most sequential design problems, an exact solution is prohibitive. We propose a simulation-based approximation that uses decision boundaries. We apply the method to RNA-seq, microarray, and reverse-phase protein array studies and show its potential advantages. The approach has been added to the Bioconductor package gaga

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut

Luther-Emery Phase and Atomic-Density Waves in a Trapped Fermion Gas

The Luther-Emery liquid is a state of matter that is predicted to occur in one-dimensional systems of interacting fermions and is characterized by a gapless charge spectrum and a gapped spin spectrum. In this Letter we discuss a realization of the Luther-Emery phase in a trapped cold-atom gas. We study by means of the density-matrix renormalization-group technique a two-component atomic Fermi gas with attractive interactions subject to parabolic trapping inside an optical lattice. We demonstrate how this system exhibits compound phases characterized by the coexistence of spin pairing and atomic-density waves. A smooth crossover occurs with increasing magnitude of the atom-atom attraction to a state in which tightly bound spin-singlet dimers occupy the center of the trap. The existence of atomic-density waves could be detected in the elastic contribution to the light-scattering diffraction pattern.Comment: 10 pages, 3 figures, 1 Table, submitted to Phys. Rev. on July 25th 200

Hispanismo y becquerianismo en José Martí.

Sin resume

Diffraction in time of a confined particle and its Bohmian paths

Diffraction in time of a particle confined in a box which its walls are removed suddenly at $t=0$ is studied. The solution of the time-dependent Schr\"{o}dinger equation is discussed analytically and numerically for various initial wavefunctions. In each case Bohmian trajectories of the particles are computed and also the mean arrival time at a given location is studied as a function of the initial state.Comment: 8 pages, 6 figure