Removing noise from pyrosequenced amplicons

Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs) present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms

Converting sporting capacity to entrepreneurial capacity: A process perspective

Managing a personal sporting career and conducting an entrepreneurial initiative are two vitally connected processes. Most athletes require a second career and many engage in entrepreneurship. Research on the similarities and differences of the sports career management process and entrepreneurial process with a special emphasis on the necessary capacities will have a ready audience among practitioners. This study begins the task of closing a surprising gap. In entrepreneurship literature, there is (1) growing research on entrepreneurial process and entrepreneurial capacity as the key driver; (2) strong work in generic, descriptive and explanatory modelling of process as a whole and capacity as a sub-process; and (3) the presence of a generic model of entrepreneurial process based of what distinguishes entrepreneurial capacity from other human capacities. In sports management literature, these research strands are virtually absent. The study indicates how the deficiency might be remedied

Self-gravitating clouds of generalized Chaplygin and modified anti-Chaplygin Gases

The Chaplygin gas has been proposed as a possible dark energy, dark matter candidate. As a working fluid in a Friedmann-Robertson-Walker universe, it exhibits early behavior reminiscent of dark matter, but at later times is more akin to a cosmological constant. In any such universe, however, one can expect local perturbations to form. Here we obtain the general equations for a self-gravitating relativistic Chaplygin gas. We solve these equations and obtain the mass-radius relationship for such structures, showing that only in the phantom regime is the mass-radius relationship large enough to be a serious candidate for highly compact massive objects at the galaxy core. In addition, we study the cosmology of a modified anti-Chaplygin gas. A self-gravitating cloud of this matter is an exact solution to Einstein's equations.Comment: 16 page

Magneto-Acoustic Waves of Small Amplitude in Optically Thin Quasi-Isentropic Plasmas

The evolution of quasi-isentropic magnetohydrodynamic waves of small but finite amplitude in an optically thin plasma is analyzed. The plasma is assumed to be initially homogeneous, in thermal equilibrium and with a straight and homogeneous magnetic field frozen in. Depending on the particular form of the heating/cooling function, the plasma may act as a dissipative or active medium for magnetoacoustic waves, while Alfven waves are not directly affected. An evolutionary equation for fast and slow magnetoacoustic waves in the single wave limit, has been derived and solved, allowing us to analyse the wave modification by competition of weakly nonlinear and quasi-isentropic effects. It was shown that the sign of the quasi-isentropic term determines the scenario of the evolution, either dissipative or active. In the dissipative case, when the plasma is first order isentropically stable the magnetoacoustic waves are damped and the time for shock wave formation is delayed. However, in the active case when the plasma is isentropically overstable, the wave amplitude grows, the strength of the shock increases and the breaking time decreases. The magnitude of the above effects depends upon the angle between the wave vector and the magnetic field. For hot (T > 10^4 K) atomic plasmas with solar abundances either in the interstellar medium or in the solar atmosphere, as well as for the cold (T < 10^3 K) ISM molecular gas, the range of temperature where the plasma is isentropically unstable and the corresponding time and length-scale for wave breaking have been found.Comment: 14 pages, 10 figures. To appear in ApJ January 200

Hydroxyl as a Tracer of H2 in the Envelope of MBM40

We observed 51 positions in the OH 1667 MHz main line transitions in the translucent, high latitude cloud MBM40. We detected OH emission in 8 out of 8 positions in the molecular core of the cloud and 24 out of 43 in the surrounding, lower extinction envelope and periphery of the cloud. Using a linear relationship between the integrated OH line intensity and E(B-V), we estimate the mass in the core, the envelope, and the periphery of the cloud to be 4, 8, and 5 solar masses. As much as a third of the total cloud mass may be found in the in the periphery (E(B-V) $<$ 0.12 mag) and about a half in the envelope (0.12 $\le$ E(B-V) $\le$ 0.17 mag). If these results are applicable to other translucent clouds the OH 1667 MHz line is an excellent tracer of gas in very low extinction regions and high-sensitivity mapping of the envelopes of molecular clouds may reveal the presence of significant quantities of molecular mass.Comment: 26 pages, 3 figures, and 5 table

Multi--Pressure Polytropes as Models for the Structure and Stability of Molecular Clouds. I. Theory

Molecular clouds are supported by thermal pressure, magnetic pressure, and turbulent pressure. Each of these can be modeled with a polytropic equation of state, so that overall the total pressure is the sum of the individual components. We model the turbulent pressure as being due to a superposition of Alfven waves. The theory of polytropes is generalized to allow for the flow of entropy in response to a perturbation, as expected for the entropy associated with wave pressure. The equation of state of molecular clouds is "soft", so that the properties of the clouds are generally governed by the conditions at the surface. In general, the polytropes are not isentropic, and this permits large density and pressure drops to occur between the center and the edge of the polytropes, as is observed.Comment: Submitted to ApJ with 10 figure

CH 3 GHz Observations of the Galactic Center

A 3 $\times$ 3 map of the Galactic Center was made at 9\arcmin resolution and 10\arcmin spacing in the CH $^2\Pi_{1/2}$, J=1/2, F=1-1 transition at 3335 MHz. The CH emission shows a velocity extent that is nearly that of the CO(1-0) line, but the CH line profiles differ markedly from the CO. The 3335 MHz CH transition primarily traces low-density molecular gas and our observations indicate that the mass of this component within $\sim$ 30 pc of the Galactic Center is $\sim$ 9 $\times$ 10$^6$ M$_\odot$. The CO-H$_2$ conversion factor obtained for the low-density gas in the mapped region is greater than that thought to apply to the dense molecular gas at the Galactic Center. In addition to tracing the low-density molecular gas at the Galactic Center, the CH spectra show evidence of emission from molecular clouds along the line of sight both in the foreground and background. The scale height of these clouds ranges from 27 - 109 pc, consistent with previous work based on observations of molecular clouds in the inner Galaxy.Comment: 29 pages, 12 figure

CN and HCN in Dense Interstellar Clouds

We present a theoretical investigation of CN and HCN molecule formation in dense interstellar clouds. We study the gas-phase CN and HCN production efficiencies from the outer photon-dominated regions (PDRs) into the opaque cosmic-ray dominated cores. We calculate the equilibrium densities of CN and HCN, and of the associated species C+, C, and CO, as functions of the far-ultraviolet (FUV) optical depth. We consider isothermal gas at 50 K, with hydrogen particle densities from 10^2 to 10^6 cm^-3. We study clouds that are exposed to FUV fields with intensities 20 to 2*10^5 times the mean interstellar FUV intensity. We assume cosmic-ray H2 ionization rates ranging from 5*10^-17 s^-1, to an enhanced value of 5*10^-16 s^-1. We also examine the sensitivity of the density profiles to the gas-phase sulfur abundance.Comment: Accepted for publication in ApJ, 33 pages, 8 figure

Radio Recombination Lines in Galactic HII Regions

We report radio recombination line (RRL) and continuum observations of a sample of 106 Galactic HII regions made with the NRAO 140 Foot radio telescope in Green Bank, WV. We believe this to be the most sensitive RRL survey ever made for a sample this large. Most of our source integration times range between 6 and 90 hours which yield typical r.m.s. noise levels of 1.0--3.5 milliKelvins. Our data result from two different experiments performed, calibrated, and analyzed in similar ways. A CII survey was made at 3.5 cm wavelength to obtain accurate measurements of carbon radio recombination lines. When combined with atomic (CI) and molecular (CO) data, these measurements will constrain the composition, structure, kinematics, and physical properties of the photodissociation regions that lie on the edges of HII regions. A second survey was made at 3.5 cm wavelength to determine the abundance of 3He in the interstellar medium of the Milky Way. Together with measurements of the 3He+ hyperfine line we get high precision RRL parameters for H, 4He, and C. Here we discuss significant improvements in these data, with both longer integrations and newly observed sources.Comment: LaTeX, 50 pages with 11 figures. Accepted for publication in The Astrophysical Journal Supplement Serie

Herschel observations of extra-ordinary sources: Detecting spiral arm clouds by CH absorption lines

We have observed CH absorption lines ($J=3/2, N=1 \leftarrow J=1/2, N=1$) against the continuum source Sgr~B2(M) using the \textit{Herschel}/HIFI instrument. With the high spectral resolution and wide velocity coverage provided by HIFI, 31 CH absorption features with different radial velocities and line widths are detected and identified. The narrower line width and lower column density clouds show `spiral arm' cloud characteristics, while the absorption component with the broadest line width and highest column density corresponds to the gas from the Sgr~B2 envelope. The observations show that each `spiral arm' harbors multiple velocity components, indicating that the clouds are not uniform and that they have internal structure. This line-of-sight through almost the entire Galaxy offers unique possibilities to study the basic chemistry of simple molecules in diffuse clouds, as a variety of different cloud classes are sampled simultaneously. We find that the linear relationship between CH and H$_2$ column densities found at lower $A_V$ by UV observations does not continue into the range of higher visual extinction. There, the curve flattens, which probably means that CH is depleted in the denser cores of these clouds.Comment: Accepted for publication in A&A, HIFI Special Issu