945 research outputs found
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
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 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 ( 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 day timescales and 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 and a dispersion measure of . 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
- …