Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds

Probing the jet base of the blazar PKS1830-211 from the chromatic variability of its lensed images. Serendipitous ALMA observations of a strong gamma-ray flare

The launching mechanism of the jets of active galactic nuclei is observationally poorly constrained, due to the large distances to these objects and the very small scales (sub-parsec) involved. In order to better constrain theoretical models, it is especially important to get information from the region close to the physical base of the jet, where the plasma acceleration takes place. In this paper, we report multi-epoch and multi-frequency continuum observations of the z=2.5 blazar PKS1830-211 with ALMA, serendipitously coincident with a strong $\gamma$-ray flare reported by Fermi-LAT. The blazar is lensed by a foreground z=0.89 galaxy, with two bright images of the compact core separated by 1". Our ALMA observations individually resolve these two images (although not any of their substructures), and we study the change of their relative flux ratio with time (four epochs spread over nearly three times the time delay between the two lensed images) and frequency (between 350 and 1050 GHz, rest-frame of the blazar), during the $\gamma$-ray flare. In particular, we detect a remarkable frequency-dependent behaviour of the flux ratio, which implies the presence of a chromatic structure in the blazar (i.e., a core-shift effect). We rule out the possiblity of micro- and milli-lensing effects and propose instead a simple model of plasmon ejection in the blazar's jet to explain the time and frequency variability of the flux ratio. We suggest that PKS1830-211 is likely one of the best sources to probe the activity at the base of a blazar's jet at submillimeter wavelengths, thanks to the peculiar geometry of the system. The implications of the core-shift in absorption studies of the foreground z=0.89 galaxy (e.g., constraints on the cosmological variations of fundamental constants) are discussed.Comment: Accepted for publication in A&

Large-Deviation Functions for Nonlinear Functionals of a Gaussian Stationary Markov Process

We introduce a general method, based on a mapping onto quantum mechanics, for investigating the large-T limit of the distribution P(r,T) of the nonlinear functional r[V] = (1/T)\int_0^T dT' V[X(T')], where V(X) is an arbitrary function of the stationary Gaussian Markov process X(T). For T tending to infinity at fixed r we find that P(r,T) behaves as exp[-theta(r) T], where theta(r) is a large deviation function. We present explicit results for a number of special cases, including the case V(X) = X \theta(X) which is related to the cooling and the heating degree days relevant to weather derivatives.Comment: 8 page

An ALMA Early Science survey of molecular absorption lines toward PKS1830-211 -- Analysis of the absorption profiles

We present the first results of an ALMA spectral survey of strong absorption lines for common interstellar species in the z=0.89 molecular absorber toward the lensed blazar PKS1830-211. The dataset brings essential information on the structure and composition of the absorbing gas in the foreground galaxy. In particular, we find absorption over large velocity intervals (gtrsim 100 km/s) toward both lensed images of the blazar. This suggests either that the galaxy inclination is intermediate and that we sample velocity gradients or streaming motions in the disk plane, that the molecular gas has a large vertical distribution or extraplanar components, or that the absorber is not a simple spiral galaxy but might be a merger system. The number of detected species is now reaching a total of 42 different species plus 14 different rare isotopologues toward the SW image, and 14 species toward the NE line-of-sight. The abundances of CH, H2O, HCO+, HCN, and NH3 relative to H2 are found to be comparable to those in the Galactic diffuse medium. Of all the lines detected so far toward PKS1830-211, the ground-state line of ortho-water has the deepest absorption. We argue that ground-state lines of water have the best potential for detecting diffuse molecular gas in absorption at high redshift.Comment: Accepted for publication in A&

Hyperglycemia and risk of ventricular tachycardia among patients hospitalized with acute myocardial infarction

BACKGROUND: Little is known about the association of hyperglycemia Tranwith the development of ventricular tachycardia (VT) in patients hospitalized with acute myocardial infarction (AMI) which we examined in the present study. The objectives of this community-wide observational study were to examine the relation between elevated serum glucose levels at the time of hospital admission for AMI and occurrence of VT, and time of occurrence of VT, during the patient\u27s acute hospitalization. METHODS: We used data from a population-based study of patients hospitalized with AMI at all central Massachusetts medical centers between 2001 and 2011. Hyperglycemia was defined as a serum glucose level \u3e /= 140 mg/dl at the time of hospital admission. The development of VT was identified from physicians notes and electrocardiographic findings by our trained team of data abstractors. RESULTS: The average age of the study population was 70 years, 58.0% were men, and 92.7% were non-Hispanic whites. The mean and median serum glucose levels at the time of hospital admission were 171.4 mg/dl and 143.0, respectively. Hyperglycemia was present in 51.9% of patients at the time of hospital admission; VT occurred in 652 patients (15.8%), and two-thirds of these episodes occurred during the first 48 h after hospital admission (early VT). After multivariable adjustment, patients with hyperglycemia were at increased risk for developing VT (adjusted OR = 1.48, 95% CI = 1.23-1.78). The presence of hyperglycemia was significantly associated with early (multivariable adjusted OR = 1.39, 95% CI = 1.11-1.73) but not with late VT. Similar associations were observed in patients with and without diabetes and in patients with and without ST-segment elevation AMI. CONCLUSIONS: Efforts should be made to closely monitor and treat patients who develop hyperglycemia, especially early after hospital admission, to reduce their risk of VT

Self-similar stable processes arising from high-density limits of occupation times of particle systems

We extend results on time-rescaled occupation time fluctuation limits of the $(d,\alpha, \beta)$-branching particle system $(0<\alpha \leq 2, 0<\beta \leq 1)$ with Poisson initial condition. The earlier results in the homogeneous case (i.e., with Lebesgue initial intensity measure) were obtained for dimensions $d>\alpha / \beta$ only, since the particle system becomes locally extinct if $d\le \alpha / \beta$. In this paper we show that by introducing high density of the initial Poisson configuration, limits are obtained for all dimensions, and they coincide with the previous ones if $d>\alpha/\beta$. We also give high-density limits for the systems with finite intensity measures (without high density no limits exist in this case due to extinction); the results are different and harder to obtain due to the non-invariance of the measure for the particle motion. In both cases, i.e., Lebesgue and finite intensity measures, for low dimensions ($d<\alpha(1+\beta)/\beta$ and $d<\alpha(2+\beta)/(1+\beta)$, respectively) the limits are determined by non-L\'evy self-similar stable processes. For the corresponding high dimensions the limits are qualitatively different: ${\cal S}'(R^d)$-valued L\'evy processes in the Lebesgue case, stable processes constant in time on $(0,\infty)$ in the finite measure case. For high dimensions, the laws of all limit processes are expressed in terms of Riesz potentials. If $\beta=1$, the limits are Gaussian. Limits are also given for particle systems without branching, which yields in particular weighted fractional Brownian motions in low dimensions. The results are obtained in the setup of weak convergence of S'(R^d)$-valued processes.Comment: 28 page

MetAMOS: A modular and open source metagenomic assembly and analysis pipeline

© 2013 Treangen et al. We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS

Connecting does not necessarily mean learning: Course handbooks as mediating tools in school-university partnerships

This is the author's accepted manuscript (titled "Course handbooks as mediating tools in learning to teach"). The final published article is available from the link below. Copyright @ 2011 American Association of Colleges for Teacher Education.Partnerships between schools and universities in England use course handbooks to guide student teacher learning during long field experiences. Using data from a yearlong ethnographic study of a postgraduate certificate of education programme in one English university, the function of course handbooks in mediating learning in two high school subject departments (history and modern foreign languages) is analyzed. Informed by Cultural Historical Activity Theory, the analysis focuses on the handbooks as mediating tools in the school-based teacher education activity systems. Qualitative differences in the mediating functions of the handbooks-in-use are examined and this leads to a consideration of the potential of such tools for teacher learning in school–university partnerships. Following Zeichner’s call for rethinking the relationships between schools and universities, the article argues that strong structural connections between different institutional sites do not necessarily enhance student teacher learning

Residence Time Statistics for Normal and Fractional Diffusion in a Force Field

We investigate statistics of occupation times for an over-damped Brownian particle in an external force field. A backward Fokker-Planck equation introduced by Majumdar and Comtet describing the distribution of occupation times is solved. The solution gives a general relation between occupation time statistics and probability currents which are found from solutions of the corresponding problem of first passage time. This general relationship between occupation times and first passage times, is valid for normal Markovian diffusion and for non-Markovian sub-diffusion, the latter modeled using the fractional Fokker-Planck equation. For binding potential fields we find in the long time limit ergodic behavior for normal diffusion, while for the fractional framework weak ergodicity breaking is found, in agreement with previous results of Bel and Barkai on the continuous time random walk on a lattice. For non-binding potential rich physical behaviors are obtained, and classification of occupation time statistics is made possible according to whether or not the underlying random walk is recurrent and the averaged first return time to the origin is finite. Our work establishes a link between fractional calculus and ergodicity breaking.Comment: 12 page

A Search for OH Megamasers at z > 0.1. III. The Complete Survey

We present the final results from the Arecibo Observatory OH megamaser survey. We discuss in detail the properties of the remaining 18 OH megamasers detected in the survey, including 3 redetections. We place upper limits on the OH emission from 85 nondetections and examine the properties of 25 ambiguous cases for which the presence or absence of OH emission could not be determined. The complete survey has discovered 50 new OH megamasers (OHMs) in (ultra)luminous infrared galaxies ([U]LIRGs) which doubles the sample of known OHMs and increases the sample at z>0.1 sevenfold. The Arecibo OH megamaser survey indicates that the OHM fraction in LIRGs is an increasing function of the far-IR luminosity (L_{FIR}) and far-IR color, reaching a fraction of roughly one third in the warmest ULIRGs. Significant relationships between OHMs and their hosts are few, primarily due to a mismatch in size scales of measured properties and an intrinsic scatter in OHM properties roughly equal to the span of the dataset. We investigate relationships between OHMs and their hosts with a variety of statistical tools including survival analysis, partial correlation coefficients, and a principal component analysis. There is no apparent OH megamaser ``fundamental plane.'' We compile data on all previously known OHMs and evaluate the possible mechanisms and relationships responsible for OHM production in merging systems. The OH-FIR relationship is reexamined using the doubled OHM sample and found to be significantly flatter than previously thought: L_{OH} ~ L_{FIR}^{1.2 +/- 0.1}. This near-linear dependence suggests a mixture of saturated and unsaturated masers, either within individual galaxies or across the sample.Comment: 28 pages, 14 figures, accepted by AJ. (AASTeX, includes emulateapj5 and onecolfloat5