Gene set bagging for estimating replicability of gene set analyses

Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach, called gene set bagging, for measuring the stability of ranking procedures using predefined gene sets. Gene set bagging involves resampling the original high-throughput data, performing gene-set analysis on the resampled data, and confirming that biological categories replicate. This procedure can be thought of as bootstrapping gene-set analysis and can be used to determine which are the most reproducible gene sets. Results: Here we apply this approach to two common genomics applications: gene expression and DNA methylation. Even with state-of-the-art statistical ranking procedures, significant categories in a gene set enrichment analysis may be unstable when subjected to resampling. Conclusions: We demonstrate that gene lists are not necessarily stable, and therefore additional steps like gene set bagging can improve biological inference of gene set analysis.Comment: 3 Figure

Cloud-scale RNA-sequencing differential expression analysis with Myrna

As sequencing throughput approaches dozens of gigabases per day, there is a growing need for efficient software for analysis of transcriptome sequencing (RNA-Seq) data. Myrna is a cloud-computing pipeline for calculating differential gene expression in large RNA-Seq datasets. We apply Myrna to the analysis of publicly available data sets and assess the goodness of fit of standard statistical models. Myrna is available from http://bowtie-bio.sf.net/myrna

Charge Pumping in Carbon Nanotubes

We demonstrate charge pumping in semiconducting carbon nanotubes by a traveling potential wave. From the observation of pumping in the nanotube insulating state we deduce that transport occurs by packets of charge being carried along by the wave. By tuning the potential of a side gate, transport of either electron or hole packets can be realized. Prospects for the realization of nanotube based single-electron pumps are discussed

Prognostic relevance of dynamic hyperinflation during cardiopulmonary exercise testing in adult patients with cystic fibrosis

AbstractBackgroundDynamic hyperinflation during cardiopulmonary exercise testing (CPET) in cystic fibrosis (CF) has not been well characterized, and little is known regarding its prevalence, risk factors and clinical associations.MethodsCPET data from 109 adult patients with mild-to-moderate CF was used, in this retrospective study, to characterize and determine the prevalence of dynamic hyperinflation, and evaluate its relationship with lung function and exercise tolerance, clinical symptoms, and prognosis over a two-year period.Results58% of patients responded to CPET with dynamic hyperinflation. These patients had significantly lower lung function (FEV1 66±19 versus 79±18%pred., p<0.01) and exercise tolerance (peak oxygen uptake 28.7±8.1 versus 32.9±6.1mL·kg−1·min−1, p=0.02), and experienced greater shortness of breath at peak exercise (7±3 versus 5±2 Modified Borg scale, p=0.04) compared to patients who responded without dynamic hyperinflation. Significant relationships between FEV1, FVC, FEV1/FVC, FEF25–75 and dynamic hyperinflation were shown (p<0.01; p=0.02; p<0.01; p<0.01, respectively). Dynamic hyperinflation was also significantly correlated with oxygen uptake, tidal volume, work-rate and shortness of breath at peak exercise (p=0.03; p<0.01; p<0.01; p=0.04, respectively). Responding to CPET with or without dynamic hyperinflation did not significantly predict FEV1 at 2years beyond the FEV1 at baseline (p=0.06), or increase the likelihood of experiencing a pulmonary exacerbation over a two-year period (p=0.24).ConclusionThe prevalence of dynamic hyperinflation during CPET in adult patients with mild-to-moderate CF is high, and is associated with reduced lung function and exercise tolerance, and increased exertional dyspnea. However, identifying dynamic hyperinflation during CPET had limited prognostic value for lung function and pulmonary exacerbation

Dynamics of dispersive single qubit read-out in circuit quantum electrodynamics

The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.Comment: Revised version: corrected typos, 8 pages, 6 figures, version with high resolution figures available at http://qudev.ethz.ch/content/science/PubsPapers.htm