MOJAVE: Monitoring of Jets in Active Galactic Nuclei with VLBA Experiments. VI. Kinematics Analysis of a Complete Sample of Blazar Jets

We discuss the jet kinematics of a complete flux-density-limited sample of 135 radio-loud active galactic nuclei (AGN) resulting from a 13 year program to investigate the structure and evolution of parsec-scale jet phenomena. Our analysis is based on new 2 cm Very Long Baseline Array (VLBA) images obtained between 2002 and 2007, but includes our previously published observations made at the same wavelength, and is supplemented by VLBA archive data. In all, we have used 2424 images spanning the years 1994-2007 to study and determine the motions of 526 separate jet features in 127 jets. The data quality and temporal coverage (a median of 15 epochs per source) of this complete AGN jet sample represents a significant advance over previous kinematics surveys. In all but five AGNs, the jets appear one-sided, most likely the result of differential Doppler boosting. In general the observed motions are directed along the jet ridge line, outward from the optically thick core feature. We directly observe changes in speed and/or direction in one third of the well-sampled jet components in our survey. While there is some spread in the apparent speeds of separate features within an individual jet, the dispersion is about three times smaller than the overall dispersion of speeds among all jets. This supports the idea that there is a characteristic flow that describes each jet, which we have characterized by the fastest observed component speed. The observed maximum speed distribution is peaked at ~10c, with a tail that extends out to ~50c. This requires a distribution of intrinsic Lorentz factors in the parent population that range up to ~50. We also note the presence of some rare low-pattern speeds or even stationary features in otherwise rapidly flowing jets... (abridged)Comment: 19 pages, 10 figures, 2 tables, accepted by the Astronomical Journal; online only material is available from http://www.cv.nrao.edu/2cmVLBA/pub/MOJAVE_VI_suppl.zi

MOJAVE: Monitoring of Jets in AGN with VLBA Experiments. VII. Blazar Jet Acceleration

We discuss acceleration measurements for a large sample of extragalactic radio jets from the MOJAVE program which studies the parsec-scale jet structure and kinematics of a complete, flux-density-limited sample of Active Galactic Nuclei (AGN). Accelerations are measured from the apparent motion of individual jet features or "components" which may represent patterns in the jet flow. We find that significant accelerations are common both parallel and perpendicular to the observed component velocities. Parallel accelerations, representing changes in apparent speed, are generally larger than perpendicular acceleration that represent changes in apparent direction. The trend for larger parallel accelerations indicates that a significant fraction of these changes in apparent speed are due to changes in intrinsic speed of the component rather than changes in direction to the line of sight. We find an overall tendency for components with increasing apparent speed to be closer to the base of their jets than components with decreasing apparent speed. This suggests a link between the observed pattern motions and the underlying flow which, in some cases, may increase in speed close to the base and decrease in speed further out; however, common hydro-dynamical processes for propagating shocks may also play a role. About half of the components show "non-radial" motion, or a misalignment between the component's structural position angle and its velocity direction, and these misalignments generally better align the component motion with the downstream emission. Perpendicular accelerations are closely linked with non-radial motion. When observed together, perpendicular accelerations are usually in the correct direction to have caused the observed misalignment.Comment: 17 pages, 11 figures, 1 table, accepted by the Astrophysical Journa

An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches

BACKGROUND: Operation of the immune system is multivariate. Reduction of the dimensionality is essential to facilitate understanding of this complex biological system. One multi-dimensional facet of the immune system is the binding of epitopes to the MHC-I and MHC-II molecules by diverse populations of individuals. Prediction of such epitope binding is critical and several immunoinformatic strategies utilizing amino acid substitution matrices have been designed to develop predictive algorithms. Contemporaneously, computational and statistical tools have evolved to handle multivariate and megavariate analysis, but these have not been systematically deployed in prediction of MHC binding. Partial least squares analysis, principal component analysis, and associated regression techniques have become the norm in handling complex datasets in many fields. Over two decades ago Wold and colleagues showed that principal components of amino acids could be used to predict peptide binding to cellular receptors. We have applied this observation to the analysis of MHC binding, and to derivation of predictive methods applicable on a whole proteome scale. RESULTS: We show that amino acid principal components and partial least squares approaches can be utilized to visualize the underlying physicochemical properties of the MHC binding domain by using commercially available software. We further show the application of amino acid principal components to develop both linear partial least squares and non-linear neural network regression prediction algorithms for MHC-I and MHC-II molecules. Several visualization options for the output aid in understanding the underlying physicochemical properties, enable confirmation of earlier work on the relative importance of certain peptide residues to MHC binding, and also provide new insights into differences among MHC molecules. We compared both the linear and non-linear MHC binding prediction tools to several predictive tools currently available on the Internet. CONCLUSIONS: As opposed to the highly constrained user-interaction paradigms of web-server approaches, local computational approaches enable interactive analysis and visualization of complex multidimensional data using robust mathematical tools. Our work shows that prediction tools such as these can be constructed on the widely available JMP(® )platform, can operate in a spreadsheet environment on a desktop computer, and are capable of handling proteome-scale analysis with high throughput

Movement Behavior of Radio-Tagged European Starlings in Urban, Rural, and Exurban Landscapes

Since their intentional introduction into the United States in the 1800s, European starlings (Sturnus vulgaris) have become the fourth most common bird species and a nuisance bird pest in both urban and rural areas. Managers require better information about starling movement and habit-use patterns to effectively manage starling populations and the damage they cause. Thus, we revisited 6 radio-telemetry studies conducted during fall or winter between 2005 and 2010 to compare starling movements (n = 63 birds) and habitat use in 3 landscapes. Switching of roosting and foraging sites in habitat-sparse rural landscapes caused daytime (0900–1500 hours) radio fixes to be on average 2.6 to 6.3 times further from capture sites than either urban or exurban landscapes (P \u3c 0.001). Roosts in urban city centers were smaller (100,000 birds) 6–13 km away in industrial zones. Radio-tagged birds from city-center roosts occasionally switched to the outlying major roosts. A multitrack railroad overpass and a treed buffer zone were used as major roosts in urban landscapes. Birds traveling to roosts from primary foraging sites in exurban and rural landscapes would often pass over closer-lying minor roosts to reach major roosts in stands of emergent vegetation in large wetlands. Daytime minimum convex polygons ranged from 101–229 km2 (x̄ = 154 km2). Anthropogenic food resources (e.g., concentrated animal feeding operations, shipping yards, landfills, and abattoirs) were primary foraging sites. Wildlife resource managers can use this information to predict potential roosting and foraging sites and average areas to monitor when implementing programs in different landscapes. In addition to tracking roosting flights, we recommend viewing high-resolution aerial images to identify potential roosting and foraging habitats before implementing lethal culls (e.g., toxicant baiting)

Full-Stokes polarimetry with circularly polarized feeds - Sources with stable linear and circular polarization in the GHz regime

We present a pipeline that allows recovering reliable information for all four Stokes parameters with high accuracy. Its novelty relies on the treatment of the instrumental effects already prior to the computation of the Stokes parameters contrary to conventional methods, such as the M\"uller matrix one. The instrumental linear polarization is corrected across the whole telescope beam and significant Stokes $Q$ and $U$ can be recovered even when the recorded signals are severely corrupted. The accuracy we reach in terms of polarization degree is of the order of 0.1-0.2 %. The polarization angles are determined with an accuracy of almost 1$^{\circ}$. The presented methodology was applied to recover the linear and circular polarization of around 150 Active Galactic Nuclei. The sources were monitored from July 2010 to April 2016 with the Effelsberg 100-m telescope at 4.85 GHz and 8.35 GHz with a cadence of around 1.2 months. The polarized emission of the Moon was used to calibrate the polarization angle. Our analysis showed a small system-induced rotation of about 1$^{\circ}$ at both observing frequencies. Finally, we identify five sources with significant and stable linear polarization; three sources remain constantly linearly unpolarized over the period we examined; a total of 11 sources have stable circular polarization degree $m_\mathrm{c}$ and four of them with non-zero $m_\mathrm{c}$. We also identify eight sources that maintain a stable polarization angle over the examined period. All this is provided to the community for polarization observations reference. We finally show that our analysis method is conceptually different from the traditionally used ones and performs better than the M\"uller matrix method. Although it was developed for a system equipped with circularly polarized feeds it can easily be modified for systems with linearly polarized feeds as well.Comment: 19 pages, 17 figures, accepted for publication in Astronomy & Astrophysics on May 30, 201

A change in the quiescent X-ray spectrum of the neutron star low-mass X-ray binary MXB 1659-29

The quasi-persistent neutron star low-mass X-ray binary MXB 1659-29 went into quiescence in 2001, and we have followed its quiescent X-ray evolution since. Observations over the first 4 years showed a rapid drop in flux and temperature of the neutron star atmosphere, interpreted as cooling of the neutron star crust which had been heated during the 2.5 year outburst. However, observations taken approximately 1400 and 2400 days into quiescence were consistent with each other, suggesting the crust had reached thermal equilibrium with the core. Here we present a new Chandra observation of MXB 1659-29 taken 11 years into quiescence and 4 years since the last Chandra observation. This new observation shows an unexpected factor of ~3 drop in count rate and change in spectral shape since the last observation, which cannot be explained simply by continued cooling. Two possible scenarios are that either the neutron star temperature has remained unchanged and there has been an increase in the column density, or, alternatively the neutron star temperature has dropped precipitously and the spectrum is now dominated by a power-law component. The first scenario may be possible given that MXB 1659-29 is a near edge-on system, and an increase in column density could be due to build-up of material in, and a thickening of, a truncated accretion disk during quiescence. But, a large change in disk height may not be plausible if standard accretion disk theory holds during quiescence. Alternatively, the disk may be precessing, leading to a higher column density during this latest observation.Comment: 6 pages, 4 figures, accepted for publication in Ap