Surveying the Dynamic Radio Sky with the Long Wavelength Demonstrator Array

This paper presents a search for radio transients at a frequency of 73.8 MHz (4 m wavelength) using the all-sky imaging capabilities of the Long Wavelength Demonstrator Array (LWDA). The LWDA was a 16-dipole phased array telescope, located on the site of the Very Large Array in New Mexico. The field of view of the individual dipoles was essentially the entire sky, and the number of dipoles was sufficiently small that a simple software correlator could be used to make all-sky images. From 2006 October to 2007 February, we conducted an all-sky transient search program, acquiring a total of 106 hr of data; the time sampling varied, being 5 minutes at the start of the program and improving to 2 minutes by the end of the program. We were able to detect solar flares, and in a special-purpose mode, radio reflections from ionized meteor trails during the 2006 Leonid meteor shower. We detected no transients originating outside of the solar system above a flux density limit of 500 Jy, equivalent to a limit of no more than about 10^{-2} events/yr/deg^2, having a pulse energy density >~ 1.5 x 10^{-20} J/m^2/Hz at 73.8 MHz for pulse widths of about 300 s. This event rate is comparable to that determined from previous all-sky transient searches, but at a lower frequency than most previous all-sky searches. We believe that the LWDA illustrates how an all-sky imaging mode could be a useful operational model for low-frequency instruments such as the Low Frequency Array, the Long Wavelength Array station, the low-frequency component of the Square Kilometre Array, and potentially the Lunar Radio Array.Comment: 20 pages; accepted for publication in A

Renal Survival in Children with Glomerulonephritis with Crescents: A Pediatric Nephrology Research Consortium Cohort Study

There is no evidence-based definition for diagnosing crescentic glomerulonephritis. The prognostic implications of crescentic lesions on kidney biopsy have not been quantified. Our objective was to determine risk factors for end-stage kidney disease (ESKD) in patients with glomerulonephritis and crescents on kidney biopsy. A query of the Pediatric Nephrology Research Consortium’s Pediatric Glomerulonephritis with Crescents registry identified 305 patients from 15 centers. A retrospective cohort study was performed with ESKD as the primary outcome. Median age at biopsy was 11 years (range 1–21). The percentage of crescents was 3–100% (median 20%). Etiologies included IgA nephropathy (23%), lupus (21%), IgA vasculitis (19%) and ANCA-associated GN (13%), post-infectious GN (5%), and anti-glomerular basement membrane disease (3%). The prevalence of ESKD was 12% at one year and 16% at last follow-up (median = 3 years, range 1–11). Median time to ESKD was 100 days. Risk factors for ESKD included %crescents, presence of fibrous crescents, estimated GFR, and hypertension at biopsy. For each 1% increase in %crescents, there was a 3% decrease in log odds of 1-year renal survival (p = 0.003) and a 2% decrease in log odds of renal survival at last follow-up (p \u3c 0.001). These findings provide an evidence base for enrollment criteria for crescentic glomerulonephritis in future clinical trials

New Limits on the Low-frequency Radio Transient Sky Using 31 hr of All-sky Data with the OVRO-LWA

We present the results of the first transient survey from the Owens Valley Radio Observatory Long Wavelength Array (OVRO–LWA) using 31 hr of data, in which we place the most constraining limits on the instantaneous transient surface density at timescales of 13 s to a few minutes and at frequencies below 100 MHz. The OVRO–LWA is a dipole array that images the entire viewable hemisphere with 58 MHz of bandwidth from 27 to 84 MHz at 13 s cadence. No transients are detected above a 6.5σ flux density limit of 10.5 Jy, implying an upper limit to the transient surface density of 2.5 × 10⁻⁸ deg⁻² at the shortest timescales probed, which is orders of magnitude deeper than has been achieved at sub-100 MHz frequencies and comparable flux densities to date. The nondetection of transients in the OVRO–LWA survey, particularly at minutes-long timescales, allows us to place further constraints on the rate of the potential population of transients uncovered by Stewart et al. From their transient rate, we expect a detection of 8.4^(+31.8)_(-8.0) events, and the probability of our null detection is 1.9^(+644)_(-1.9) x 10⁻³, ruling out a transient rate >1.4 × 10⁻⁴ days⁻¹ deg⁻² with 95% confidence at a flux density limit of 18.1 Jy, under the assumption of a flat spectrum and wide bandwidth. We discuss the implications of our nondetection for this population and further constraints that can be made on the source spectral index, intrinsic emission bandwidth, and resulting luminosity distribution

The 74MHz System on the Very Large Array

The Naval Research Laboratory and the National Radio Astronomy Observatory completed implementation of a low frequency capability on the VLA at 73.8 MHz in 1998. This frequency band offers unprecedented sensitivity (~25 mJy/beam) and resolution (~25 arcsec) for low-frequency observations. We review the hardware, the calibration and imaging strategies, comparing them to those at higher frequencies, including aspects of interference excision and wide-field imaging. Ionospheric phase fluctuations pose the major difficulty in calibrating the array. Over restricted fields of view or at times of extremely quiescent ionospheric ``weather'', an angle-invariant calibration strategy can be used. In this approach a single phase correction is devised for each antenna, typically via self-calibration. Over larger fields of view or at times of more normal ionospheric ``weather'' when the ionospheric isoplanatic patch size is smaller than the field of view, we adopt a field-based strategy in which the phase correction depends upon location within the field of view. This second calibration strategy was implemented by modeling the ionosphere above the array using Zernike polynomials. Images of 3C sources of moderate strength are provided as examples of routine, angle-invariant calibration and imaging. Flux density measurements indicate that the 74 MHz flux scale at the VLA is stable to a few percent, and tied to the Baars et al. value of Cygnus A at the 5 percent level. We also present an example of a wide-field image, devoid of bright objects and containing hundreds of weaker sources, constructed from the field-based calibration. We close with a summary of lessons the 74 MHz system offers as a model for new and developing low-frequency telescopes. (Abridged)Comment: 73 pages, 46 jpeg figures, to appear in ApJ

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5′ and 3′ half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized

NGC6240: Merger-Induced Star Formation & Gas Dynamics

We present spatially resolved integral field spectroscopic K-band data at a resolution of 0.13" (60pc) and interferometric CO(2-1) line observations of the prototypical merging system NGC6240. Despite the clear rotational signature, the stellar kinematics in the two nuclei are dominated by dispersion. We use Jeans modelling to derive the masses and the mass-to-light ratios of the nuclei. Combining the luminosities with the spatially resolved Br-gamma equivalent width shows that only 1/3 of the K-band continuum from the nuclei is associated with the most recent star forming episode; and that less than 30% of the system's bolometric luminosity and only 9% of its stellar mass is due to this starburst. The star formation properties, calculated from typical merger star formation histories, demonstrate the impact of different assumptions about the star formation history. The properties of the nuclei, and the existence of a prominent old stellar population, indicate that the nuclei are remnants of the progenitor galaxies' bulges.Comment: 18 pages, 14 figures. Accepted for publication in A&

Exclusive Photoproduction of the Cascade (Xi) Hyperons

We report on the first measurement of exclusive Xi-(1321) hyperon photoproduction in gamma p --> K+ K+ Xi- for 3.2 < E(gamma) < 3.9 GeV. The final state is identified by the missing mass in p(gamma,K+ K+)X measured with the CLAS detector at Jefferson Laboratory. We have detected a significant number of the ground-state Xi-(1321)1/2+, and have estimated the total cross section for its production. We have also observed the first excited state Xi-(1530)3/2+. Photoproduction provides a copious source of Xi's. We discuss the possibilities of a search for the recently proposed Xi5-- and Xi5+ pentaquarks.Comment: submitted to Phys. Rev.

Carbocyanine Dye Usage in Demarcating Boundaries of the Aged Human Red Nucleus

Background: Though the adult human magnocellular Red nucleus (mNr) is essentially vestigial and its boundaries with neighbouring structures have never been well demarcated, human studies in utero have shown a well developed semilunar mNr wrapping around the caudal parvicellular Red nucleus (pNr), similar to what is seen in quadrupeds. In the present study, we have sought to better delineate the morphological determinants of the adult human Red nucleus (ahRn). Methods and Findings: Serial sections of ahRn show fine myelinated fibers arising from pNr and turning toward the central tegmental tract. DiI was deposited within a well restricted region of ahRn at the fasciculus retroflexus level and the extent of label determined. Nissl-stained serial sections allowed production of a 3-D mNr model, showing rudimentary, vestigial morphology compared with its well developed infant homologue. DiI within this vestigial mNr region at the level of the oculomotor nerve showed labeled giant/large mNr neurons, coarse fiber bundles at the ventral tegmental decussation and lateral lemniscal label. Conclusions: Large amounts of DiI and a long incubation time have proven useful in aged human brain as a marker of long axons and large cell bodies of projecting neurons such as the rubrospinal projection and for clarifying nuclear boundaries of closed nuclei (e.g., the large human pNr). Our 3D model of adult human mNr appeared shrunken in shape and axiall

A robust measure of correlation between two genes on a microarray

<p>Abstract</p> <p>Background</p> <p>The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to experimental conditions could be co-expressed and show similar patterns of expression on a microarray. Using any of a variety of clustering methods or gene network analyses we can partition genes of interest into groups, clusters, or modules based on measures of similarity. Typically, Pearson correlation is used to measure distance (or similarity) before implementing a clustering algorithm. Pearson correlation is quite susceptible to outliers, however, an unfortunate characteristic when dealing with microarray data (well known to be typically quite noisy.)</p> <p>Results</p> <p>We propose a resistant similarity metric based on Tukey's biweight estimate of multivariate scale and location. The resistant metric is simply the correlation obtained from a resistant covariance matrix of scale. We give results which demonstrate that our correlation metric is much more resistant than the Pearson correlation while being more efficient than other nonparametric measures of correlation (e.g., Spearman correlation.) Additionally, our method gives a systematic gene flagging procedure which is useful when dealing with large amounts of noisy data.</p> <p>Conclusion</p> <p>When dealing with microarray data, which are known to be quite noisy, robust methods should be used. Specifically, robust distances, including the biweight correlation, should be used in clustering and gene network analysis.</p