Proteomics FASTA Archive and Reference Resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58584/1/1756_ftp.pd

Formation of phase lags at the cyclotron energies in the pulse profiles of magnetized, accreting neutron stars

Context: Accretion-powered X-ray pulsars show highly energy-dependent and complex pulse-profile morphologies. Significant deviations from the average pulse profile can appear, in particular close to the cyclotron line energies. These deviations can be described as energy-dependent phase lags, that is, as energy-dependent shifts of main features in the pulse profile. Aims: Using a numerical study we explore the effect of cyclotron resonant scattering on observable, energy-resolved pulse profiles. Methods: We generated the observable emission as a function of spin phase, using Monte Carlo simulations for cyclotron resonant scattering and a numerical ray-tracing routine accounting for general relativistic light-bending effects on the intrinsic emission from the accretion columns. Results: We find strong changes in the pulse profile coincident with the cyclotron line energies. Features in the pulse profile vary strongly with respect to the average pulse profile with the observing geometry and shift and smear out in energy additionally when assuming a non-static plasma. Conclusions: We demonstrate how phase lags at the cyclotron energies arise as a consequence of the effects of angular redistribution of X-rays by cyclotron resonance scattering in a strong magnetic field combined with relativistic effects. We also show that phase lags are strongly dependent on the accretion geometry. These intrinsic effects will in principle allow us to constrain a system's accretion geometry.Comment: 4 pages, 4 figures; updated reference lis

Cyclotron resonant scattering feature simulations. I. Thermally averaged cyclotron scattering cross sections, mean free photon-path tables, and electron momentum sampling

Electron cyclotron resonant scattering features (CRSFs) are observed as absorption-like lines in the spectra of X-ray pulsars. A significant fraction of the computing time for Monte Carlo simulations of these quantum mechanical features is spent on the calculation of the mean free path for each individual photon before scattering, since it involves a complex numerical integration over the scattering cross section and the (thermal) velocity distribution of the scattering electrons. We aim to numerically calculate interpolation tables which can be used in CRSF simulations to sample the mean free path of the scattering photon and the momentum of the scattering electron. The tables also contain all the information required for sampling the scattering electron's final spin. The tables were calculated using an adaptive Simpson integration scheme. The energy and angle grids were refined until a prescribed accuracy is reached. The tables are used by our simulation code to produce artificial CRSF spectra. The electron momenta sampled during these simulations were analyzed and justified using theoretically determined boundaries. We present a complete set of tables suited for mean free path calculations of Monte Carlo simulations of the cyclotron scattering process for conditions expected in typical X-ray pulsar accretion columns (0.01<B/B_{crit}<=0.12, where B_{crit}=4.413x10^{13} G and 3keV<=kT<15keV). The sampling of the tables is chosen such that the results have an estimated relative error of at most 1/15 for all points in the grid. The tables are available online at http://www.sternwarte.uni-erlangen.de/research/cyclo.Comment: A&A, in pres

W. C. Falkner to H. R. Miller (29 April 1861)

Concerning outrage at the decision to move troops and separate the regiment

Character Displacement in the Midst of Substantial Background Evolution in Anolis Lizard Island Populations

Negative interactions between species can generate divergent selection that causes character displacement. However, other processes cause similar divergence. We use spatial and temporal replication across island populations of Anolis lizards to assess the importance of negative interactions in driving trait shifts. Previous work showed that the establishment of Anolis sagrei on islands drove resident Anolis carolinensis to perch higher and evolve larger toepads. To further test the interaction\u27s causality and predictability, we resurveyed a subset of islands nine years later. Anolis sagrei had established on one island between surveys. We found that A. carolinensis on this island now perch higher and have larger toepads. However, toepad morphology change on this island was not distinct from shifts on six other islands whose Anolis community composition had not changed. Thus, the presence of A. sagrei only partly explains A. carolinensis trait variation across space and time. We also found that A. carolinensis on islands with previously established A. sagrei now perch higher than a decade ago, and that current A. carolinensis perch height is correlated with A. sagrei density. Our results suggest that character displacement likely interacts with other evolutionary processes in this system, and that temporal data are key to detecting such interactions

The effect of price increases on predicted alcohol purchasing decisions and choice to substitute

Introduction: Few studies have undertaken to explore whether people who consume particular alcoholic beverages have a greater tendency to substitute with cheaper alcohol in response to price increases. The aim of this study was to investigate the effect of price increases on alcohol purchasing decisions, specifically the influence on brand and cross-beverage substitution across demographic, drinking level and socio-economic factors. Method: Data on participants’ alcohol purchasing habits and consumption were collected via an online survey, including their reactions to three price increases to alcoholic beverages types previously purchased. Data were analysed using logistic regression, with substitution behaviour the dependent variable, controlling for demographic and socio-economic factors. Results: Responses to different price increases varied by drinking level, which was consistently and significantly associated with likelihood of substitution behaviour across beverage types. For a 50% increase in price, regardless of whether participants purchased beer, wine, bottled spirits or premixed spirits, drinking at levels which put participants at high risk of short-term harms was associated with a higher likelihood of substitution with cheaper brands or beverage types (OR: 1.729; OR: 1.787; OR: 1.729 and OR: 1.729, respectively). Conclusions: No consistent trends in responses occurred according to respondent characteristics, suggesting that increasing price may be an effective tool to influence purchasing behaviour across the population. Results also suggested that those who drink at levels which put them at high risk of short-term harms may be more likely to circumvent price increases by switching to a cheaper product

A diagrammatic view of the equals sign: arithmetical equivalence as a means, not an end

It is recommended in the mathematics education literature that pupils be presented with equality statements that can be assessed for numerical balance by attending to notational structure rather than computation. I describe an alternative, diagrammatic approach in which pupils do not assess statements but instead use them to make substitutions of notation. I report on two trials of a computer-based task conducted with pairs of pupils and highlight two findings. First, the pupils found it useful to articulate the distinct substitutive effects of commutative (‘swap’, ‘switch’) and partitional (‘split’, ‘separate’) statements when working on the task. Secondly, the pupils did not notice that some of the statements presented were in fact false, which suggests their substituting activities were independent of numerical equivalence conceptions. This demonstrates that making substitutions offers task designers a mathematical utility for equality statements that is distinct from, but complementary to, assessing numerical balance