Consistent Testing for Recurrent Genomic Aberrations

Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated with tumor development or progression. A number of tools have been proposed to assess the statistical significance of recurrent DNA copy number aberrations, but their statistical properties have not been carefully studied. Cyclic shift testing, a permutation procedure using independent random shifts of genomic marker observations on the genome, has been proposed to identify recurrent aberrations, and is potentially useful for a wider variety of purposes, including identifying regions with methylation aberrations or overrepresented in disease association studies. For data following a countable-state Markov model, we prove the asymptotic validity of cyclic shift $p$-values under a fixed sample size regime as the number of observed markers tends to infinity. We illustrate cyclic shift testing for a variety of data types, producing biologically relevant findings for three publicly available datasets.Comment: 35 pages, 7 figure

OFF-SITE COSTS OF SOIL EROSION: A CASE STUDY IN THE WILLAMETTE VALLEY

This study attempts to provide relative magnitudes of average and marginal costs of off-site sediment-related costs in OregonÂ’s Willamette Valley. Water treatment; road, river channel, and dam maintenance; and hydroelectric generation are examined. Road maintenance and water treatment are nonnegligible average cost items. These costs should not be interpreted as justification for erosion control as marginal cost estimates for water treatment indicate the controls on the margin would yield roughly one-third the average cost.Land Economics/Use,

Ocean shrimp report 1979 season

Statewide Pacific ocean shrimp, Pandalus jordani, landings totaled 2,237.7 mt (4,922,857 lb), down 3,745 mt (8,240,386 lb) from the 1978 catch of 5,983.3 mt (13,163,243 lb). The 1979 landings are the lowest since 1976 when 1,545.5 mt (3,400,191 lb) were landed. Area A (Eureka-Crescent City)landings dropped to 1,842.5 mt (4,053,605 lb) from 5,046.3 mt (11,101,895 lb) landed during the previous season. No landings were made in Area B-1 (Fort Bragg). Only 2.0 mt (4,385 lb) were reported caught in Area B-2 (Bodega Bay). Record landings of 393.1 mt (864,867 lb) were made in Area C (Morro Bay-Avila), surpassing the previous record of 90.4 mt (199,000 lb) landed in 1953. In Area A a record 71 vessels, 34 double-rigged and 37 single-rigged, shrimped during the season. Average catch per hour was a low .15 mt (338 lb) and .22 mt (490 1b) for single-rig and double-rig vessels, respectively. In Area C average catch per hour was .23 mt (508 lb) and .42 mt (924 lb) for single-rig and double-rig vessels, respectively. Area A shrimp catches were dominated by 1-year-old shrimp throughout most of the season. The age composition in Area C shifted predominately from 2-year-old shrimp in May and June to predominately 1-year-old shrimp in July, August, October, and November. Area A was closed for one month from July 15 to August 15 because closure criteria of less than .16 mt (350 lb) per hour for two consecutive weeks was met and year class composition exceeded 70% of 1-year-old shrimp. The season was closed October 14 when the catch per hour criterion was exceeded again. (18pp.

A stacking method to study the gamma-ray emission of source samples based on the co-adding of Fermi LAT count maps

We present a stacking method that makes use of co-added maps of gamma-ray counts produced from data taken with the Fermi Large Area Telescope. Sources with low integrated gamma-ray fluxes that are not detected individually may become detectable when their corresponding count maps are added. The combined data set is analyzed with a maximum likelihood method taking into account the contribution from point-like and diffuse background sources. For both simulated and real data, detection significance and integrated gamma-ray flux are investigated for different numbers of stacked sources using the public Fermi Science Tools for analysis and data preparation. The co-adding is done such that potential source signals add constructively, in contrast to the signals from background sources, which allows the stacked data to be described with simply structured models. We show, for different scenarios, that the stacking method can be used to increase the cumulative significance of a sample of sources and to characterize the corresponding gamma-ray emission. The method can, for instance, help to search for gamma-ray emission from galaxy clusters.Comment: accepted for publication in Astronomy & Astrophysics, 10 pages, 12 figure

Absolute Calibration of the Radio Astronomy Flux Density Scale at 22 to 43 GHz Using Planck

The Planck mission detected thousands of extragalactic radio sources at frequencies from 28 to 857 GHz. Planck's calibration is absolute (in the sense that it is based on the satellite's annual motion around the Sun and the temperature of the cosmic microwave background), and its beams are well characterized at sub-percent levels. Thus Planck's flux density measurements of compact sources are absolute in the same sense. We have made coordinated VLA and ATCA observations of 65 strong, unresolved Planck sources in order to transfer Planck's calibration to ground-based instruments at 22, 28, and 43 GHz. The results are compared to microwave flux density scales currently based on planetary observations. Despite the scatter introduced by the variability of many of the sources, the flux density scales are determined to 1-2% accuracy. At 28 GHz, the flux density scale used by the VLA runs 3.6% +- 1.0% below Planck values; at 43 GHz, the discrepancy increases to 6.2% +- 1.4% for both ATCA and the VLA.Comment: 16 pages, 4 figures and 4 table

Reflectance of Polytetrafluoroethylene (PTFE) for Xenon Scintillation Light

Gaseous and liquid xenon particle detectors are being used in a number of applications including dark matter search and neutrino-less double beta decay experiments. Polytetrafluoroethylene (PTFE) is often used in these detectors both as electrical insulator and as a light reflector to improve the efficiency of detection of scintillation photons. However, xenon emits in the vacuum ultraviolet wavelength region (175 nm) where the reflecting properties of PTFE are not sufficiently known. In this work we report on measurements of PTFE reflectance, including its angular distribution, for the xenon scintillation light. Various samples of PTFE, manufactured by different processes (extruded, expanded, skived and pressed) have been studied. The data were interpreted with a physical model comprising both specular and diffuse reflections. The reflectance obtained for these samples ranges from about 47% to 66% for VUV light. Fluoropolymers, namely ETFE, FEP and PFA were also measured

Tightly Correlated HI and FUV Emission in the Outskirts of M83

We compare sensitive HI data from The HI Nearby Galaxy Survey (THINGS) and deep far UV (FUV) data from GALEX in the outer disk of M83. The FUV and HI maps show a stunning spatial correlation out to almost 4 optical radii (r25), roughly the extent of our maps. This underscores that HI traces the gas reservoir for outer disk star formation and it implies that massive (at least low level) star formation proceeds almost everywhere HI is observed. Whereas the average FUV intensity decreases steadily with increasing radius before leveling off at ~1.7 r25, the decline in HI surface density is more subtle. Low HI columns (<2 M_solar/pc^2) contribute most of the mass in the outer disk, which is not the case within r25. The time for star formation to consume the available HI, inferred from the ratio of HI to FUV intensity, rises with increasing radius before leveling off at ~100 Gyr, i.e., many Hubble times, near ~1.7 r25. Assuming the relatively short H2 depletion times observed in the inner parts of galaxies hold in outer disks, the conversion of HI into bound, molecular clouds seems to limit star formation in outer galaxy disks. The long consumption times suggest that most of the extended HI observed in M83 will not be consumed by in situ star formation. However, even these low star formation rates are enough to expect moderate chemical enrichment in a closed outer disk.Comment: Accepted for Publication in ApJ

Assimilation of GPM-Retrieved Marine Surface Meteorology Variables for Two Winter Storms

No abstract availabl