The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data

Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce Learner of Functional Enrichment (LeFE), a statistical/machine learning algorithm based on Random Forest, and demonstrate it on several diverse datasets: smoker/never smoker, breast cancer classification, and cancer drug sensitivity. We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant functional themes consistent with known biology

Electron Spin Resonance at the Level of 10000 Spins Using Low Impedance Superconducting Resonators

We report on electron spin resonance (ESR) measurements of phosphorus donors localized in a 200 square micron area below the inductive wire of a lumped element superconducting resonator. By combining quantum limited parametric amplification with a low impedance microwave resonator design we are able to detect around 20000 spins with a signal-to-noise ratio (SNR) of 1 in a single shot. The 150 Hz coupling strength between the resonator field and individual spins is significantly larger than the 1 - 10 Hz coupling rates obtained with typical coplanar waveguide resonator designs. Due to the larger coupling rate, we find that spin relaxation is dominated by radiative decay into the resonator and dependent upon the spin-resonator detuning, as predicted by Purcell

Tail emission from a ring-like jet: its application to shallow decays of early afterglows and to GRB 050709

Similar to the pulsar, the magnetic axis and the spin axis of the gamma-ray burst source may not lie on the same line. This may cause a ring-like jet due to collimation of the precessing magnetic axis. We analyze the tail emission from such a jet, and find that it has a shallow decay phase with temporal index equal to -1/2 if the Lorentz factor of the ejecta is not very high. This phase is consistent with the shallow decay phase of some early X-ray afterglow detected by {\it{swift}}. The ring-like jet has a tail cusp with sharp rising and very sharp decay. This effect can provide an explanation for the re-brightening and sharp decay of the X-ray afterglow of GRB 050709.Comment: 6 pages, 2 figures. Accepted by ChJA

Observation of Entanglement Between Itinerant Microwave Photons and a Superconducting Qubit

A localized qubit entangled with a propagating quantum field is well suited to study non-local aspects of quantum mechanics and may also provide a channel to communicate between spatially separated nodes in a quantum network. Here, we report the on demand generation and characterization of Bell-type entangled states between a superconducting qubit and propagating microwave fields composed of zero, one and two-photon Fock states. Using low noise linear amplification and efficient data acquisition we extract all relevant correlations between the qubit and the photon states and demonstrate entanglement with high fidelity.Comment: 5 pages, 3 figure