Evaluation of peak-picking algorithms for protein mass spectrometry

Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves

A Spitzer view of protoplanetary disks in the gamma Velorum cluster

We present new Spitzer Space Telescope observations of stars in the young ~5 Myr gamma Velorum stellar cluster. Combining optical and 2MASS photometry, we have selected 579 stars as candidate members of the cluster. With the addition of the Spitzer mid-infrared data, we have identified 5 debris disks around A-type stars, and 5-6 debris disks around solar-type stars, indicating that the strong radiation field in the cluster does not completely suppress the production of planetesimals in the disks of cluster members. However, we find some evidence that the frequency of circumstellar primordial disks is lower, and the IR flux excesses are smaller than for disks around stellar populations with similar ages. This could be evidence for a relatively fast dissipation of circumstellar dust by the strong radiation field from the highest mass star(s) in the cluster. Another possibility is that gamma Velorum stellar cluster is slightly older than reported ages and the the low frequency of primordial disks reflects the fast disk dissipation observed at ~5 Myr.Comment: Accepted for publication in the Astrophysical Journal: 32 pages; 11 Figure

Self-similar solution of a nonsteady problem of nonisothermal vapour condensation on a droplet growing in diffusion regime

This paper presents a mathematically exact self-similar solution to the joint nonsteady problems of vapour diffusion towards a droplet growing in a vapour-gas medium and of removal of heat released by a droplet into a vapour-gas medium during vapour condensation. An equation for the temperature of the droplet is obtained; and it is only at that temperature that the self-similar solution exists. This equation requires the constancy of the droplet temperature and even defines it unambiguously throughout the whole period of the droplet growth. In the case of strong display of heat effects, when the droplet growth rate decreases significantly, the equation for the temperature of the droplet is solved analytically. It is shown that the obtained temperature fully coincides with the one that settles in the droplet simultaneously with the settlement of its diffusion regime of growth. At the obtained temperature of the droplet the interrelated nonsteady vapour concentration and temperature profiles of the vapour-gas medium around the droplet are expressed in terms of initial (prior to the nucleation of the droplet) parameters of the vapour-gas medium. The same parameters are used to formulate the law in accordance with which the droplet is growing in diffusion regime, and also to define the time that passes after the nucleation of the droplet till the settlement of diffusion regime of droplet growth, when the squared radius of the droplet becomes proportionate to time. For the sake of completeness the case of weak display of heat effects is been studied.Comment: 12 pages, 4 figure

Precise study of the resonance at Q0=(1,0,0) in URu2Si2

New inelastic neutron scattering experiments have been performed on URu2Si2 with special focus on the response at Q0=(1,0,0), which is a clear signature of the hidden order (HO) phase of the compound. With polarized inelastic neutron experiments, it is clearly shown that below the HO temperature (T0 = 17.8 K) a collective excitation (the magnetic resonance at E0 \approx 1.7 meV) as well as a magnetic continuum co-exist. Careful measurements of the temperature dependence of the resonance lead to the observation that its position shifts abruptly in temperature with an activation law governed by the partial gap opening and that its integrated intensity has a BCS-type temperature dependence. Discussion with respect to recent theoretical development is made

Soil biochemistry and microbial activity in vineyards under conventional and organic management at Northeast Brazil.

The São Francisco Submedium Valley is located at the Brazilian semiarid region and is an important center for irrigated fruit growing. This region is responsible for 97% of the national exportation of table grapes, including seedless grapes. Based on the fact that orgThe São Francisco Submedium Valley is located at the Brazilian semiarid region and is an important center for irrigated fruit growing. This region is responsible for 97% of the national exportation of table grapes, including seedless grapes. Based on the fact that organic fertilization can improve soil quality, we compared the effects of conventional and organic soil management on microbial activity and mycorrhization of seedless grape crops. We measured glomerospores number, most probable number (MPN) of propagules, richness of arbuscular mycorrhizal fungi (AMF) species, AMF root colonization, EE-BRSP production, carbon microbial biomass (C-MB), microbial respiration, fluorescein diacetate hydrolytic activity (FDA) and metabolic coefficient (qCO2). The organic management led to an increase in all variables with the exception of EE-BRSP and qCO2. Mycorrhizal colonization increased from 4.7% in conventional crops to 15.9% in organic crops. Spore number ranged from 4.1 to 12.4 per 50 g-1 soil in both management systems. The most probable number of AMF propagules increased from 79 cm-3 soil in the conventional system to 110 cm-3 soil in the organic system. Microbial carbon, CO2 emission, and FDA activity were increased by 100 to 200% in the organic crop. Thirteen species of AMF were identified, the majority in the organic cultivation system. Acaulospora excavata, Entrophospora infrequens, Glomus sp.3 and Scutellospora sp. were found only in the organically managed crop. S. gregaria was found only in the conventional crop. Organically managed vineyards increased mycorrhization and general soil microbial activity

Biogeochemical signatures in the lichen Hypogymnia physodes in the mid Urals

Abstract Multi-element content and uranium (U) isotopes were investigated in the lichen Hypogymnia physodes (native and transplants) sampled across a 60-km transect, centred on Karabash smelter town, from Turgoyak Lake (SW) to Kyshtym (NE) to investigate the origin of U. Kyshtym was the site of a major nuclear accident in 1957. 234 U/ 238 U activity ratios in native thalli sampled during July 2001 were within the natural isotopic ratio in minerals. Uranium/thorium (U/Th) ratios were higher in native thalli towards the NE (average 0.73) than those in the SW (average 0.57). Element signatures in native thalli and transplants suggest U was derived from fossil fuel combustion from Karabash and sources lying further to the east. Systematic and significant U enrichment indicative of a nuclear fuel cycle source was not detected in any sample. Element signatures in epiphytic lichen transplants and native thalli provide a powerful method to evaluate U deposition

Mass Transfer by Stellar Wind

I review the process of mass transfer in a binary system through a stellar wind, with an emphasis on systems containing a red giant. I show how wind accretion in a binary system is different from the usually assumed Bondi-Hoyle approximation, first as far as the flow's structure is concerned, but most importantly, also for the mass accretion and specific angular momentum loss. This has important implications on the evolution of the orbital parameters. I also discuss the impact of wind accretion, on the chemical pollution and change in spin of the accreting star. The last section deals with observations and covers systems that most likely went through wind mass transfer: barium and related stars, symbiotic stars and central stars of planetary nebulae (CSPN). The most recent observations of cool CSPN progenitors of barium stars, as well as of carbon-rich post-common envelope systems, are providing unique constraints on the mass transfer processes.Comment: Chapter 7, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G. Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe

Random UV-C mutagenesis of Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars

Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 was mutagenized using UV-C irradiation to produce yeast strains for anaerobic conversion of lignocellulosic sugars to ethanol. UV-C irradiation potentially produces large numbers of random mutations broadly and uniformly over the whole genome to generate unique strains. Wild-type cultures of S. stipitis NRRL Y-7124 were subjected to UV-C (234 nm) irradiation targeted at approximately 40% cell survival. When surviving cells were selected in sufficient numbers via automated plating strategies and cultured anaerobically on xylose medium for 5 months at 28°C, five novel mutagenized S. stipitis strains were obtained. Variable number tandem repeat analysis revealed that mutations had occurred in the genome, which may have produced genes that allowed the anaerobic utilization of xylose. The mutagenized strains were capable of growing anaerobically on xylose/glucose substrate with higher ethanol production during 250- to 500-h growth than a Saccharomyces cerevisiae yeast strain that is the standard for industrial fuel ethanol production. The S. stipitis strains resulting from this intense multigene mutagenesis strategy have potential application in industrial fuel ethanol production from lignocellulosic hydrolysates

Fifty Years of IMF Variation: The Intermediate-Mass Stars

I track the history of star count estimates of the Milky Way field star and open cluster IMFs, concentrating on the neglected mass range from 1 to 15 M${_\odot}$. The prevalent belief in a universal IMF appears to be without basis for this mass range. Two recent estimates of the field star IMF using different methods and samples give values of the average logarithmic slope $\Gamma$ between -1.7 and -2.1 in the mass range 1.1 to 4 M${_\odot}$. Two older estimates between 2 and 15 M${_\odot}$ disagree severely; the field IMF in this range is essentially unknown from star counts. Variations in $\Gamma$ among open cluster IMFs in this mass range have not decreased despite numerous detailed studies, even for studies using homogeneous data and reduction procedures and including only clusters with a significant mass range. These cluster variations \textit{might} be due to the combined effects of sampling, systematic errors, stellar evolution uncertainties, dynamical evolution, and unresolved binaries. If so, then the cluster data are consistent with a universal IMF, but are also consistent with sizeable variations. The cluster data do not allow an estimate of an average IMF or $\Gamma$ because the average depends on the choice of weighting procedure and other effects. If the spread in cluster IMFs is in excess of the effects listed above, real IMF variations must occur that do not depend much on physical conditions explored so far. The complexity of the star formation process seen in observations and simulations suggests that large realization-to-realization differences might be expected, in which case an individual cluster IMF would be in part the product of evolutionary contingency in star formation, and the function of interest is the probability distribution of IMF parameters.Comment: 18 pages, including 4 figures: invited talk presented at the conference on "IMF@50: The Stellar Initial Mass Function Fifty Years Later" held at Abbazia di Spineto, Siena, Italy, May 2004; to be published by Kluwer Academic Publishers, edited by E. Corbelli, F. Palla, and H. Zinnecke

Stellar Coronal and Wind Models: Impact on Exoplanets

Surface magnetism is believed to be the main driver of coronal heating and stellar wind acceleration. Coronae are believed to be formed by plasma confined in closed magnetic coronal loops of the stars, with winds mainly originating in open magnetic field line regions. In this Chapter, we review some basic properties of stellar coronae and winds and present some existing models. In the last part of this Chapter, we discuss the effects of coronal winds on exoplanets.Comment: Chapter published in the "Handbook of Exoplanets", Editors in Chief: Juan Antonio Belmonte and Hans Deeg, Section Editor: Nuccio Lanza. Springer Reference Work