A nested mixture model for protein identification using mass spectrometry

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected to mass spectrometry, which generates thousands of spectra, each characteristic of its generating peptide. Here we consider the problem of inferring, from these spectra, which proteins and peptides are present in the sample. We develop a statistical approach to the problem, based on a nested mixture model. In contrast to commonly used two-stage approaches, this model provides a one-stage solution that simultaneously identifies which proteins are present, and which peptides are correctly identified. In this way our model incorporates the evidence feedback between proteins and their constituent peptides. Using simulated data and a yeast data set, we compare and contrast our method with existing widely used approaches (PeptideProphet/ProteinProphet) and with a recently published new approach, HSM. For peptide identification, our single-stage approach yields consistently more accurate results. For protein identification the methods have similar accuracy in most settings, although we exhibit some scenarios in which the existing methods perform poorly.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS316 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Projecting a High-School Quarterback’s Performance at the Collegiate Level: A Comparison of the Rivals, 247 Sports, and ESPN Recruiting Ratings

We examine recruiting ratings for high-school quarterbacks over the period 2006-2012 from Rivals, 247 Sports, and ESPN.  Using Lee & Preacher’s (2013) test of the difference between two dependent correlations with one variable in common and ordinary least squares regression, we determine that the Rivals ratings have the strongest correlation with quarterback performance over the time-period examined.  The 247 Sports ratings follow closely behind the Rivals ratings; however, the ESPN ratings correlate more weakly with a quarterback’s career performance in college

Photonic architecture for scalable quantum information processing in NV-diamond

Physics and information are intimately connected, and the ultimate information processing devices will be those that harness the principles of quantum mechanics. Many physical systems have been identified as candidates for quantum information processing, but none of them are immune from errors. The challenge remains to find a path from the experiments of today to a reliable and scalable quantum computer. Here, we develop an architecture based on a simple module comprising an optical cavity containing a single negatively-charged nitrogen vacancy centre in diamond. Modules are connected by photons propagating in a fiber-optical network and collectively used to generate a topological cluster state, a robust substrate for quantum information processing. In principle, all processes in the architecture can be deterministic, but current limitations lead to processes that are probabilistic but heralded. We find that the architecture enables large-scale quantum information processing with existing technology.Comment: 24 pages, 14 Figures. Comment welcom

FAPRI U.S. Agricultural Sector Elasticities, Volume I: Crops

This report presents estimates of supply, demand, and price transmission elasticities for the U.S. crops sector. The estimates are derived from the U.S. crops model maintained by the Food and Agricultural Policy Research Institute (FAPRI) and are prepared in accordance with procedures stipulated by the Organization for Economic Cooperation and Development (OECD). The first section of this report provides a general overview and describes the procedures used to perform the elasticity calculations. Each succeeding section provides general information about the elasticity estimates for a particular activity. Specific attention is given to those results that may not be intuitively clear and, in particular, to the elasticities that depend on the interaction of two or more equations in the FAPRI modeling system

FAPRI U.S. Agricultural Sector Elasticities, Volume II: Livestock, Poultry, and Dairy

This report presents estimates of supply, demand, and price transmission elasticities for the U.S. livestock, poultry, and dairy sectors. The estimates are derived from models maintained by the Food and Agricultural Policy Research Institute (FAPRI) and are prepared in accordance with procedures stipulated by the Organization for Economic Cooperation and Development (OECD)

Protostellar accretion traced with chemistry. High resolution C18O and continuum observations towards deeply embedded protostars in Perseus

Context: Understanding how accretion proceeds is a key question of star formation, with important implications for both the physical and chemical evolution of young stellar objects. In particular, very little is known about the accretion variability in the earliest stages of star formation. Aims: To characterise protostellar accretion histories towards individual sources by utilising sublimation and freeze-out chemistry of CO. Methods: A sample of 24 embedded protostars are observed with the Submillimeter Array (SMA) in context of the large program "Mass Assembly of Stellar Systems and their Evolution with the SMA" (MASSES). The size of the C$^{18}$O emitting region, where CO has sublimated into the gas-phase, is measured towards each source and compared to the expected size of the region given the current luminosity. The SMA observations also include 1.3 mm continuum data, which are used to investigate whether a link can be established between accretion bursts and massive circumstellar disks. Results: Depending on the adopted sublimation temperature of the CO ice, between 20% and 50% of the sources in the sample show extended C$^{18}$O emission indicating that the gas was warm enough in the past that CO sublimated and is currently in the process of refreezing; something which we attribute to a recent accretion burst. Given the fraction of sources with extended C$^{18}$O emission, we estimate an average interval between bursts of 20000-50000 yr, which is consistent with previous estimates. No clear link can be established between the presence of circumstellar disks and accretion bursts, however the three closest known binaries in the sample (projected separations <20 AU) all show evidence of a past accretion burst, indicating that close binary interactions may also play a role in inducing accretion variability.Comment: Accepted for publication in A&A, 21 pages, 13 figure

Insulating and Conducting Phases of RbC60

Optical measurements were performed on thin films of Rb$_{x}$C$_{60}$, identified by X-ray diffraction as mostly $x=1$ material. The samples were subjected to various heat treatments, including quenching and slow cooling from 400K. The dramatic increase in the transmission of the quenched samples, and the relaxation towards the transmission observed in slow cooled samples provides direct evidence for the existence of a metastable insulating phase. Slow cooling results in a phase transition between two electrically conducting phases.Comment: Minor revisions. Submitted to PRB, RevTeX 3.0 file, 2 postscript figures included, ir_dop

Physical and Spectral Characteristics of the T8 and Later-Type Dwarfs

We use new and published near-IR spectra, with synthetic spectra, to derive physical properties of three of the latest-type T dwarfs. A new R~1700 spectrum of the T7.5 dwarf HD 3651B, with existing data, allows a detailed comparison to the well-studied and very similar dwarf, Gl 570D. We find that HD 3651B has both higher gravity and metallicity than Gl 570D, with Teff=820-830K, log g= 5.4-5.5, [m/H]= +0.2 and Kzz=10^4cm^2/s. Its age is 8-12 Gyr and its implied mass is 60-70 M_Jup. We perform a similar analyis of the T8 and T7.5 dwarfs 2MASS J09393548-2448279 and 2MASS J11145133-2618235 using published data, comparing them to the well-studied T8, 2MASS J04151954-0935066. We find that the two dwarfs have the same Teff as the reference dwarf, and similar gravities, but lower metallicities. The parameters are Teff=725-775K and [m/H]= -0.3; log g=5.3-5.45 for 2MASS J09393548-2448279 and log g=5.0-5.3 for 2MASS J11145133- 261823. The age and mass are ~10Gyr and 60M_Jup for 2MASS J09393548-2448279, and ~5 Gyr and 40M_Jup for 2MASS J11145133-261823. A serious limitation is the incompleteness of the line lists of CH4 and NH3 at lambda <1.7um. Spectra of Saturn and Jupiter, and of laboratory CH4 and NH3 gas, suggest that NH3 features in the Y- and J-bands may be useful as indicators of the next cooler spectral type, and not features in the H- and K-bands as previously thought. However large uncertainties remain, as the abundance of NH3 is likely to be significantly below the chemical equilibrium value, and inclusion of laboratory NH3 opacities predicts band shapes that are discrepant with existing data. It is possible that the T spectral class will have to be extended to low temperatures around 400K, when water clouds condense in the atmosphere [abridged].Comment: 34 pages including 10 figures and two tables; accepted for publication in the Astrophysical Journa

Toxic metal concentrations in cigarettes obtained from U.S. smokers in 2009 : results from the International Tobacco Control (ITC) United States survey cohort

This research was funded by grants from the U.S. National Cancer Institute (R01 CA100362 and P01 CA138389), and the Canadian Institutes of Health Research (115016). Geoffrey T. Fong was supported by a Senior Investigator Award from the Ontario Institute for Cancer Research (OICR) and a Prevention Scientist Award from the Canadian Cancer Society Research Institute.Smoking-related diseases can be attributed to the inhalation of many different toxins, including heavy metals, which have a host of detrimental health effects. The current study reports the levels of arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), and lead (Pb) in cigarettes obtained from adult smokers participating in the 2009 wave of the ITC United States Survey (N = 320). The mean As, Cd, Cr, Ni, and Pb levels were 0.17, 0.86, 2.35, 2.21, and 0.44 mu g/g, respectively. There were some differences in metal concentrations of cigarette brands produced by different manufacturers, suggesting differences in the source of tobaccos used by different companies. For Ni, there were significant pairwise differences between Philip Morris U.S. (PMUSA) and R.J. Reynolds (RJR) brands (PMUSA higher; p 0.10). Because of the variety of toxic heavy metals in cigarette tobacco, and their numerous negative health effects, metal content in cigarette tobacco should be reduced.Publisher PDFPeer reviewe