Tellipsoid: Exploiting inter-gene correlation for improved detection of differential gene expression

Motivation: Algorithms for differential analysis of microarray data are vital to modern biomedical research. Their accuracy strongly depends on effective treatment of inter-gene correlation. Correlation is ordinarily accounted for in terms of its effect on significance cut-offs. In this paper it is shown that correlation can, in fact, be exploited {to share information across tests}, which, in turn, can increase statistical power. Results: Vastly and demonstrably improved differential analysis approaches are the result of combining identifiability (the fact that in most microarray data sets, a large proportion of genes can be identified a priori as non-differential) with optimization criteria that incorporate correlation. As a special case, we develop a method which builds upon the widely used two-sample t-statistic based approach and uses the Mahalanobis distance as an optimality criterion. Results on the prostate cancer data of Singh et al. (2002) suggest that the proposed method outperforms all published approaches in terms of statistical power. Availability: The proposed algorithm is implemented in MATLAB and in R. The software, called Tellipsoid, and relevant data sets are available at http://www.egr.msu.edu/~desaikeyComment: 19 pages, Submitted to Bioinformatic

A wider audience: Turning VLBI into a survey instrument

Radio observations using the Very Long Baseline Interferometry (VLBI) technique typically have fields of view of only a few arcseconds, due to the computational problems inherent in imaging larger fields. Furthermore, sensitivity limitations restrict observations to very compact and bright objects, which are few and far between on the sky. Thus, while most branches of observational astronomy can carry out sensitive, wide-field surveys, VLBI observations are limited to targeted observations of carefully selected objects. However, recent advances in technology have made it possible to carry out the computations required to target hundreds of sources simultaneously. Furthermore, sensitivity upgrades have dramatically increased the number of objects accessible to VLBI observations. The combination of these two developments have enhanced the survey capabilities of VLBI observations such that it is now possible to observe (almost) any point in the sky with milli-arcsecond resolution. In this talk I review the development of wide-field VLBI, which has made significant progress over the last three years.Comment: Invited review at the General Assembly of the Astronomische Gesellschaf

LOFAR observations of 4C+19.44. On the discovery of low frequency spectral curvature in relativistic jet knots

We present the first LOFAR observations of the radio jet in the quasar 4C+19.44 (a.k.a. PKS 1354+19) obtained with the long baselines. The achieved resolution is very well matched to that of archival Jansky Very Large Array (JVLA) observations at higher radio frequencies as well as the archival X-ray images obtained with {\it Chandra}. We found that, for several knots along the jet, the radio flux densities measured at hundreds of MHz lie well below the values estimated by extrapolating the GHz spectra. This clearly indicates the presence of spectral curvature. Radio spectral curvature has been already observed in different source classes and/or extended radio structures and it has been often interpreted as due to intrinsic processes, as a curved particle energy distribution, rather than absorption mechanisms ({ Razin-Tsytovich} effect, free-free or synchrotron self absorption to name a few). Here we discuss our results according to the scenario where particles undergo stochastic acceleration mechanisms also in quasar jet knots.Comment: 13 pages, 4 tables, 4 figures, pre-proof version, published on the Astrophysical Journal (Harris, et al. 2019 ApJ, 873, 21

DiFX2: A more flexible, efficient, robust and powerful software correlator

Software correlation, where a correlation algorithm written in a high-level language such as C++ is run on commodity computer hardware, has become increasingly attractive for small to medium sized and/or bandwidth constrained radio interferometers. In particular, many long baseline arrays (which typically have fewer than 20 elements and are restricted in observing bandwidth by costly recording hardware and media) have utilized software correlators for rapid, cost-effective correlator upgrades to allow compatibility with new, wider bandwidth recording systems and improve correlator flexibility. The DiFX correlator, made publicly available in 2007, has been a popular choice in such upgrades and is now used for production correlation by a number of observatories and research groups worldwide. Here we describe the evolution in the capabilities of the DiFX correlator over the past three years, including a number of new capabilities, substantial performance improvements, and a large amount of supporting infrastructure to ease use of the code. New capabilities include the ability to correlate a large number of phase centers in a single correlation pass, the extraction of phase calibration tones, correlation of disparate but overlapping sub-bands, the production of rapidly sampled filterbank and kurtosis data at minimal cost, and many more. The latest version of the code is at least 15% faster than the original, and in certain situations many times this value. Finally, we also present detailed test results validating the correctness of the new code.Comment: 28 pages, 9 figures, accepted for publication in PAS

On Pulsar Distance Measurements and their Uncertainties

Accurate distances to pulsars can be used for a variety of studies of the Galaxy and its electron content. However, most distance measures to pulsars have been derived from the absorption (or lack thereof) of pulsar emission by Galactic HI gas, which typically implies that only upper or lower limits on the pulsar distance are available. We present a critical analysis of all measured HI distance limits to pulsars and other neutron stars, and translate these limits into actual distance estimates through a likelihood analysis that simultaneously corrects for statistical biases. We also apply this analysis to parallax measurements of pulsars in order to obtain accurate distance estimates and find that the parallax and HI distance measurements are biased in different ways, because of differences in the sampled populations. Parallax measurements typically underestimate a pulsar's distance because of the limited distance to which this technique works and the consequential strong effect of the Galactic pulsar distribution (i.e. the original Lutz-Kelker bias), in HI distance limits, however, the luminosity bias dominates the Lutz-Kelker effect, leading to overestimated distances because the bright pulsars on which this technique is applicable are more likely to be nearby given their brightness.Comment: 32 pages, 1 figure, 2 tables; Accepted for publication in the Astrophysical Journa

Perceptually Motivated Wavelet Packet Transform for Bioacoustic Signal Enhancement

A significant and often unavoidable problem in bioacoustic signal processing is the presence of background noise due to an adverse recording environment. This paper proposes a new bioacoustic signal enhancement technique which can be used on a wide range of species. The technique is based on a perceptually scaled wavelet packet decomposition using a species-specific Greenwood scale function. Spectral estimation techniques, similar to those used for human speech enhancement, are used for estimation of clean signal wavelet coefficients under an additive noise model. The new approach is compared to several other techniques, including basic bandpass filtering as well as classical speech enhancement methods such as spectral subtraction, Wiener filtering, and Ephraim–Malah filtering. Vocalizations recorded from several species are used for evaluation, including the ortolan bunting (Emberiza hortulana), rhesus monkey (Macaca mulatta), and humpback whale (Megaptera novaeanglia), with both additive white Gaussian noise and environment recording noise added across a range of signal-to-noise ratios (SNRs). Results, measured by both SNR and segmental SNR of the enhanced wave forms, indicate that the proposed method outperforms other approaches for a wide range of noise conditions

Nowhere to Hide: Radio-faint AGN in the GOODS-N field. I. Initial catalogue and radio properties

(Abridged) Conventional radio surveys of deep fields ordinarily have arc-second scale resolutions often insufficient to reliably separate radio emission in distant galaxies originating from star-formation and AGN-related activity. Very long baseline interferometry (VLBI) can offer a solution by identifying only the most compact radio emitting regions in galaxies at cosmological distances where the high brightness temperatures (in excess of $10^5$ K) can only be reliably attributed to AGN activity. We present the first in a series of papers exploring the faint compact radio population using a new wide-field VLBI survey of the GOODS-N field. The unparalleled sensitivity of the European VLBI Network (EVN) will probe a luminosity range rarely seen in deep wide-field VLBI observations, thus providing insights into the role of AGN to radio luminosities of the order $10^{22}~\mathrm{W\,Hz^{-1}}$ across cosmic time. The newest VLBI techniques are used to completely cover an entire 7'.5 radius area to milliarcsecond resolutions, while bright radio sources ($S > 0.1$ mJy) are targeted up to 25 arcmin from the pointing centre. Multi-source self-calibration, and a primary beam model for the EVN array are used to correct for residual phase errors and primary beam attenuation respectively. This paper presents the largest catalogue of VLBI detected sources in GOODS-N comprising of 31 compact radio sources across a redshift range of 0.11-3.44, almost three times more than previous VLBI surveys in this field. We provide a machine-readable catalogue and introduce the radio properties of the detected sources using complementary data from the e-MERLIN Galaxy Evolution survey (eMERGE).Comment: 15 pages, 8 figures, accepted in A&A. Machine-readable table available upon reques

VLA Observations of Single Pulses from the Galactic Center Magnetar

We present the results of a 7-12 GHz phased-array study of the Galactic center magnetar J1745-2900 with the Karl G. Jansky Very Large Array (VLA). Using data from two 6.5 hour observations from September 2014, we find that the average profile is comprised of several distinct components at these epochs and is stable over $\sim$day timescales and $\sim$GHz frequencies. Comparison with additional phased VLA data at 8.7 GHz shows significant profile changes on longer timescales. The average profile at 7-12 GHz is dominated by the jitter of relatively narrow pulses. The pulses in each of the four main profile components seen in September 2014 are uncorrelated in phase and amplitude, though there is a small but significant correlation in the occurrence of pulses in two of the profile components. Using the brightest pulses, we measure the dispersion and scattering parameters of J1745-2900. A joint fit of 38 pulses gives a 10 GHz pulse broadening time of $\tau_{\rm sc, 10} = 0.09 \pm 0.03~\rm ms$ and a dispersion measure of ${\rm DM} = 1760^{+2.4}_{-1.3}~{\rm pc~cm}^{-3}$. Both of these results are consistent with previous measurements, which suggests that the scattering and dispersion measure of J1745-2900 may be stable on timescales of several years.Comment: 20 pages, 10 figures, published in Ap

VLBI astrometry of PSR J2222-0137: a pulsar distance measured to 0.4% accuracy

The binary pulsar J2222-0137 is an enigmatic system containing a partially recycled millisecond pulsar and a companion of unknown nature. Whilst the low eccentricity of the system favors a white dwarf companion, an unusual double neutron star system is also a possibility, and optical observations will be able to distinguish between these possibilities. In order to allow the absolute luminosity (or upper limit) of the companion object to be properly calibrated, we undertook astrometric observations with the Very Long Baseline Array to constrain the system distance via a measurement of annual geometric parallax. With these observations, we measure the parallax of the J2222-0137 system to be 3.742 +0.013 -0.016 milliarcseconds, yielding a distance of 267.3 +1.2 -0.9 pc, and measure the transverse velocity to be 57.1 +0.3 -0.2 km/s. Fixing these parameters in the pulsar timing model made it possible to obtain a measurement of Shapiro delay and hence the system inclination, which shows that the system is nearly edge-on (sin i = 0.9985 +/- 0.0005). Furthermore, we were able to detect the orbital motion of J2222-0137 in our VLBI observations and measure the longitude of ascending node. The VLBI astrometry yields the most accurate distance obtained for a radio pulsar to date, and is furthermore the most accurate parallax for any radio source obtained at "low" radio frequencies (below ~5 GHz, where the ionosphere dominates the error budget). Using the astrometric results, we show the companion to J2222-0137 will be easily detectable in deep optical observations if it is a white dwarf. Finally, we discuss the implications of this measurement for future ultra-high-precision astrometry, in particular in support of pulsar timing arrays.Comment: 22 pages, 7 figures, accepted for publication in Ap

Detection of fast radio transients with multiple stations: a case study using the Very Long Baseline Array

Recent investigations reveal an important new class of transient radio phenomena that occur on sub-millisecond timescales. Often transient surveys' data volumes are too large to archive exhaustively. Instead, an on-line automatic system must excise impulsive interference and detect candidate events in real-time. This work presents a case study using data from multiple geographically distributed stations to perform simultaneous interference excision and transient detection. We present several algorithms that incorporate dedispersed data from multiple sites, and report experiments with a commensal real-time transient detection system on the Very Long Baseline Array (VLBA). We test the system using observations of pulsar B0329+54. The multiple-station algorithms enhanced sensitivity for detection of individual pulses. These strategies could improve detection performance for a future generation of geographically distributed arrays such as the Australian Square Kilometre Array Pathfinder and the Square Kilometre Array.Comment: 12 pages, 14 figures. Accepted for Ap