SigsPack, a package for cancer mutational signatures

BACKGROUND: Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studies, and some of them have been linked to known oncogenic processes. Identification of the processes contributing to mutations observed in a sample is potentially informative to understand the cancer etiology. RESULTS: We present here SigsPack, a Bioconductor package to estimate a sample's exposure to mutational processes described by a set of mutational signatures. The package also provides functions to estimate stability of these exposures, using bootstrapping. The performance of exposure and exposure stability estimations have been validated using synthetic and real data. Finally, the package provides tools to normalize the mutation frequencies with respect to the tri-nucleotide contents of the regions probed in the experiment. The importance of this effect is illustrated in an example. CONCLUSION: SigsPack provides a complete set of tools for individual sample exposure estimation, and for mutation catalogue & mutational signatures normalization

Toward Continuous Monitoring of Breath Biochemistry: A Paper-Based Wearable Sensor for Real-Time Hydrogen Peroxide Measurement in Simulated Breath

Exhaled breath contains a large amount of biochemical and physiological information concerning one’s health and provides an alternative route to noninvasive medical diagnosis of diseases. In the case of lung diseases, hydrogen peroxide (H2O2) is an important biomarker associated with asthma, chronic obstructive pulmonary disease, and lung cancer and can be detected in exhaled breath. The current method of breath analysis involves condensation of exhaled breath, is not continuous or real time, and requires two separate and bulky devices, complicating the periodic or long-term monitoring of a patient. We report the first disposable paper-based electrochemical wearable sensor that can monitor exhaled H2O2 in artificial breath calibration-free and continuously, in real time, and can be integrated into a commercial respiratory mask for on-site testing of exhaled breath. To improve precision for sensing H2O2, we perform differential electrochemical measurement by amperometry in which screen-printed Prussian Blue-mediated and nonmediated carbon electrodes are used for differential analysis. We were able to measure H2O2 in simulated breath in a concentration-dependent manner in real time, confirming its functionality. This proposed system is versatile, and by modifying the chemistry of the sensing electrodes, our method of differential sensing can be extended to continuous monitoring of other analytes in exhaled breath

Dynamics of the Pionium with the Density Matrix Formalism

The evolution of pionium, the $\pi^+ \pi^-$ hydrogen-like atom, while passing through matter is solved within the density matrix formalism in the first Born approximation. We compare the influence on the pionium break-up probability between the standard probabilistic calculations and the more precise picture of the density matrix formalism accounting for interference effects. We focus our general result in the particular conditions of the DIRAC experiment at CERN.Comment: 14 pages, 2 figures, submitted to J. Phys. B: At. Mol. Phy

Optimization of a high work function solution processed vanadium oxide hole-extracting layer for small molecule and polymer organic photovoltaic cells

We report a method of fabricating a high work function, solution processable vanadium oxide (V2Ox(sol)) hole-extracting layer. The atmospheric processing conditions of film preparation have a critical influence on the electronic structure and stoichiometry of the V2Ox(sol), with a direct impact on organic photovoltaic (OPV) cell performance. Combined Kelvin probe (KP) and ultraviolet photoemission spectroscopy (UPS) measurements reveal a high work function, n-type character for the thin films, analogous to previously reported thermally evaporated transition metal oxides. Additional states within the band gap of V2Ox(sol) are observed in the UPS spectra and are demonstrated using X-ray photoelectron spectroscopy (XPS) to be due to the substoichiometric nature of V2Ox(sol). The optimized V2Ox(sol) layer performance is compared directly to bare indium–tin oxide (ITO), poly(ethyleneoxythiophene):poly(styrenesulfonate) (PEDOT:PSS), and thermally evaporated molybdenum oxide (MoOx) interfaces in both small molecule/fullerene and polymer/fullerene structures. OPV cells incorporating V2Ox(sol) are reported to achieve favorable initial cell performance and cell stability attributes

SOCIAL CONSTRAINTS ON ADULT LANGUAGE LEARNING

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73181/1/j.1749-6632.1981.tb42015.x.pd

First Dark Matter Results from the XENON100 Experiment

The XENON100 experiment, in operation at the Laboratori Nazionali del Gran Sasso in Italy, is designed to search for dark matter WIMPs scattering off 62 kg of liquid xenon in an ultra-low background dual-phase time projection chamber. In this letter, we present first dark matter results from the analysis of 11.17 live days of non-blind data, acquired in October and November 2009. In the selected fiducial target of 40 kg, and within the pre-defined signal region, we observe no events and hence exclude spin-independent WIMP-nucleon elastic scattering cross-sections above 3.4 x 10^-44 cm^2 for 55 GeV/c^2 WIMPs at 90% confidence level. Below 20 GeV/c^2, this result constrains the interpretation of the CoGeNT and DAMA signals as being due to spin-independent, elastic, light mass WIMP interactions.Comment: 5 pages, 5 figures. Matches published versio

Measurement of the radiative capture cross section of the s-process branching points 204Tl and 171Tm at the n-TOF facility (CERN)

The neutron capture cross section of some unstable nuclei is especially relevant for s-process nucleosynthesis studies. This magnitude is crucial to determine the local abundance pattern, which can yield valuable information of the s-process stellar environment. In this work we describe the neutron capture (n,γ) measurement on two of these nuclei of interest, 204Tl and 171Tm, from target production to the final measurement, performed successfully at the n_TOF facility at CERN in 2014 and 2015. Preliminary results on the ongoing experimental data analysis will also be shown. These results include the first ever experimental observation of capture resonances for these two nuclei.The authors acknowledge financial support by the Spanish FPA2014-52823-C2-2-P project, by the EC Marie Curie Action “NeutAndalus” (FP7-PEOPLE-2012-CIG- 334315), by the ARGOS scholarship of the Spanish Nuclear Safety Council (CSN) and the Universitat Politècnica de Catalunya, and by the University of Sevilla via the VI PPIT-US program

Gill Function in an Elasmobranch

Highly efficient oxygen uptake in elasmobranchs, as indicated by frequent excess of PaO2 over PEO2 has previously been ascribed to the operation of multicapillary rather than counter-current gas exchange by the gills. Analysis of models shows that, at maximum efficiency, a multicapillary system cannot account for values of PaO2 greater than (PIO2+PEO2)/2. In Port Jackson sharks Heterodontus portusjacksoni) PaO2 commonly exceeds (PIO2+PEO2)/2, which indicates the operation of a functional counter-current at the respiratory surface. The anatomical basis of this counter-current is provided by the demonstration that a continuous flow of water passes between the secondary lamellae into septal canals and thence via the parabranchial cavities to the exterior