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 novel search for gravitationally lensed radio sources in wide-field VLBI imaging from the mJIVE-20 survey

We present a novel pilot search for gravitational lenses in the mJIVE-20 survey, which observed $24\,903$ radio sources selected from FIRST with the VLBA at an angular resolution of 5 mas. We have taken the visibility data for an initial $3\,640$ sources that were detected by the mJIVE-20 observations and re-mapped them to make wide-field images, selecting fourteen sources that had multiple components separated by $\geq100$ mas, with a flux-ratio of $\leq15$:$1$ and a surface brightness consistent with gravitational lensing. Two of these candidates are re-discoveries of gravitational lenses found as part of CLASS. The remaining twelve candidates were then re-observed at 1.4 GHz and then simultaneously at 4.1 and 7.1 GHz with the VLBA to measure the spectral index and surface brightness of the individual components as a function of frequency. Ten were rejected as core-jet or core-hotspot(s) systems, with surface brightness distributions and/or spectral indices inconsistent with gravitational lensing, and one was rejected after lens modelling demonstrated that the candidate lensed images failed the parity test. The final lens candidate has an image configuration that is consistent with a simple lens mass model, although further observations are required to confirm the lensing nature. Given the two confirmed gravitational lenses in the mJIVE-20 sample, we find a robust lensing-rate of $1$:($318\pm225$) for a statistical sample of 635 radio sources detected on mas-scales, which is consistent with that found for CLASS.Comment: 31 pages, 22 figures; accepted for publication in MNRA

Optimising the length of doped polymer light mixers

Transparent Refractive Index Matched Micro-particles (TRIMM) in polymer rods are highly efficient light mixers. This paper addressess the problem of estimating the optimum length fr the mixing rods, for a given TRIMM-to-matrix refractive index ratio and concentration. Light mixing can be this maximised and loss minimised, without computer ray tracing simulations. The probability density function and mean angle for a single TRIMM sphere ray deviation are derived and used in modelling an expression for a critical mixer length for rays of normal incidence. Similar models could be very useful design tools with further development

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

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

The First Very Long Baseline Interferometric SETI Experiment

The first Search for Extra-Terrestrial Intelligence (SETI) conducted with Very Long Baseline Interferometry (VLBI) is presented. By consideration of the basic principles of interferometry, we show that VLBI is efficient at discriminating between SETI signals and human generated radio frequency interference (RFI). The target for this study was the star Gliese 581, thought to have two planets within its habitable zone. On 2007 June 19, Gliese 581 was observed for 8 hours at 1230-1544 with the Australian Long Baseline Array. The dataset was searched for signals appearing on all interferometer baselines above five times the noise limit. A total of 222 potential SETI signals were detected and by using automated data analysis techniques, were ruled out as originating from the Gliese 581 system. From our results we place an upper limit of 7 MW/Hz on the power output of any isotropic emitter located in the Gliese 581 system, within this frequency range. This study shows that VLBI is ideal for targeted SETI, including follow-up observations. The techniques presented are equally applicable to next-generation interferometers, such as the long baselines of the Square Kilometre Array (SKA).Comment: 34 pages, 6 figures, 2 tables. Accepted on 25/05/2012 for publication in The Astronomical Journa

Reconciling optical and radio observations of the binary millisecond pulsar PSR J1640+2224

Previous optical and radio observations of the binary millisecond pulsar PSR J1640+2224 have come to inconsistent conclusions about the identity of its companion, with some observations suggesting the companion is a low-mass helium-core (He-core) white dwarf (WD), while others indicate it is most likely a high-mass carbon-oxygen (CO) WD. Binary evolution models predict PSR J1640+2224 most likely formed in a low-mass X-ray binary (LMXB) based on the pulsar's short spin period and long-period, low-eccentricity orbit, in which case its companion should be a He-core WD with mass about $0.35 - 0.39 \, M_\odot$, depending on metallicity. If it is instead a CO WD, that would suggest the system has an unusual formation history. In this paper we present the first astrometric parallax measurement for this system from observations made with the Very Long Baseline Array (VLBA), from which we determine the distance to be $1520^{+170}_{-150}\,\mathrm{pc}$. We use this distance and a reanalysis of archival optical observations originally taken in 1995 with the Wide Field Planetary Camera 2 (WFPC2) on the Hubble Space Telescope (HST) in order to measure the WD's mass. We also incorporate improvements in calibration, extinction model, and WD cooling models. We find that the existing observations are not sufficient to tightly constrain the companion mass, but we conclude the WD mass is $>0.4\,M_\odot$ with $>90\%$ confidence. The limiting factor in our analysis is the low signal-to-noise ratio of the original HST observations.Comment: 6 pages, 5 figure

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