Revealing the Structure of an Accretion Disk Through Energy Dependent X-ray Microlensing

We present results from monitoring observations of the gravitationally lensed quasar RX J1131-1231 performed with the Chandra X-ray Observatory. The X-ray observations were planned with relatively long exposures that allowed a search for energy-dependent microlensing in the soft (0.2-2 keV) and hard (2-10 keV) light curves of the images of RX J1131-1231. We detect significant microlensing in the X-ray light-curves of images A and D, and energy-dependent microlensing of image D. The magnification of the soft band appears to be larger than that in the hard band by a factor of ~ 1.3 when image D becomes more magnified. This can be explained by the difference between a compact, softer-spectrum corona that is producing a more extended, harder spectrum reflection component off the disk. This is supported by the evolution of the fluorescent iron line in image D over three consecutive time-averaged phases of the light curve. In the first period, a Fe line at E = 6.36(-0.16,+0.13) keV is detected (at > 99% confidence). In the second period, two Fe lines are detected, one at E = 5.47(-0.08,+0.06) keV (detected at > 99% confidence) and another at E = 6.02(-0.07,+0.09) keV (marginally detected at > 90% confidence), and in the third period, a broadened Fe line at 6.42(-0.15,+0.19) keV is detected (at > 99% confidence). This evolution of the Fe line profile during the microlensing event is consistent with the line distortion expected when a caustic passes over the inner disk where the shape of the fluorescent Fe line is distorted by General Relativistic and Doppler effects.Comment: 20 pages, includes 10 figures, submitted to Ap

X-Ray and Optical Flux Anomalies in the Quadruply Lensed QSO 1RXS J1131-1231

Optical and X-ray observations of the quadruply imaged quasar 1RXS J1131-1231 show flux ratio anomalies among the images factors of ~2 in the optical and \~3-9 in X-rays. Temporal variability of the quasar seems an unlikely explanation for the discrepancies between the X-ray and optical flux ratio anomalies. The negative parity of the most affected image and the decreasing trend of the anomalies with wavelength suggest microlensing as a possible explanation; this would imply that the source of optical radiation in RXS J1131 is ~10^4 R_g in size for a black hole mass of ~10^8 M_sun. We also present evidence for different X-ray spectral hardness ratios among the four images.Comment: 5 pages, 1 color figure, replaced with version accepted to Ap

A Robust Determination of the size of quasar accretion disks using gravitational microlensing

Using microlensing measurements from a sample of 27 image-pairs of 19 lensed quasars we determine a maximum likelihood estimate for the accretion disk size of an {{\em}average} quasar of $r_s=4.0^{+2.4}_{-3.1}$ light days at rest frame $=1736$\AA\ for microlenses with a mean mass of $=0.3M_\odot$. This value, in good agreement with previous results from smaller samples, is roughly a factor of 5 greater than the predictions of the standard thin disk model. The individual size estimates for the 19 quasars in our sample are also in excellent agreement with the results of the joint maximum likelihood analysis.Comment: 6 pages, 3 figures, submitted to Ap

I. Flux and color variations of the quadruply imaged quasar HE 0435-1223

aims: We present VRi photometric observations of the quadruply imaged quasar HE 0435-1223, carried out with the Danish 1.54m telescope at the La Silla Observatory. Our aim was to monitor and study the magnitudes and colors of each lensed component as a function of time. methods: We monitored the object during two seasons (2008 and 2009) in the VRi spectral bands, and reduced the data with two independent techniques: difference imaging and PSF (Point Spread Function) fitting.results: Between these two seasons, our results show an evident decrease in flux by ~0.2-0.4 magnitudes of the four lensed components in the three filters. We also found a significant increase (~0.05-0.015) in their V-R and R-i color indices. conclusions: These flux and color variations are very likely caused by intrinsic variations of the quasar between the observed epochs. Microlensing effects probably also affect the brightest "A" lensed component.Comment: 10 pages, 8 figure

Further Evidence that Quasar X-Ray Emitting Regions Are Compact: X-Ray and Optical Microlensing in the Lensed Quasar Q J0158-4325

We present four new seasons of optical monitoring data and six epochs of X-ray photometry for the doubly-imaged lensed quasar Q J0158-4325. The high-amplitude, short-period microlensing variability for which this system is known has historically precluded a time delay measurement by conventional methods. We attempt to circumvent this limitation by application of a Monte Carlo microlensing analysis technique, but we are only able to prove that the delay must have the expected sign (image A leads image B). Despite our failure to robustly measure the time delay, we successfully model the microlensing at optical and X-ray wavelengths to find a half light radius for soft X-ray emission log(r_{1/2,X,soft}/cm) = 14.3^{+0.4}_{-0.5}, an upper limit on the half-light radius for hard X-ray emission log(r_{1/2,X,hard}/cm) <= 14.6 and a refined estimate of the inclination-corrected scale radius of the optical R-band (rest frame 3100 Angstrom) continuum emission region of log(r_s/cm) = 15.6+-0.3.Comment: 9 pages, 6 figures, submitted to Ap

A New Microlensing Event in the Doubly-Imaged Quasar Q0957+561

We present evidence for ultraviolet/optical microlensing in the gravitationally lensed quasar Q0957+561. We combine new measurements from our optical monitoring campaign at the United States Naval Observatory, Flagstaff (USNO) with measurements from the literature and find that the time-delay-corrected r-band flux ratio m_A - m_B has increased by ~0.1 magnitudes over a period of five years beginning in the fall of 2005. We apply our Monte Carlo microlensing analysis procedure to the composite light curves, obtaining a measurement of the optical accretion disk size, log {(r_s/cm)[cos(i)/0.5]^{1/2}} = 16.2^{+0.5}_{-0.6}, that is consistent with the quasar accretion disk size - black hole mass relation.Comment: Replaced with accepted version. Minor adjustments to text but conclusions unchanged. Data in Table 2 have been updated and table now includes additional observation

COSMOGRAIL: the COSmological MOnitoring of GRAvItational Lenses IX. Time delays, lens dynamics and baryonic fraction in HE 0435-1223

We present accurate time delays for the quadruply imaged quasar HE 0435-1223. The delays were measured from 575 independent photometric points obtained in the R-band between January 2004 and March 2010. With seven years of data, we clearly show that quasar image A is affected by strong microlensing variations and that the time delays are best expressed relative to quasar image B. We measured Delta_t(BC) = 7.8+/-0.8 days, Delta_t(BD) = -6.5+/-0.7 days and Delta_t_CD = -14.3+/-0.8 days. We spacially deconvolved HST NICMOS2 F160W images to derive accurate astrometry of the quasar images and to infer the light profile of the lensing galaxy. We combined these images with a stellar population fitting of a deep VLT spectrum of the lensing galaxy to estimate the baryonic fraction, $f_b$, in the Einstein radius. We measured f_b = 0.65+0.13-0.10 if the lensing galaxy has a Salpeter IMF and f_b = 0.45+0.04-0.07 if it has a Kroupa IMF. The spectrum also allowed us to estimate the velocity dispersion of the lensing galaxy, sigma_ap = 222+/-34 km/s. We used f_b and sigma_ap to constrain an analytical model of the lensing galaxy composed of an Hernquist plus generalized NFW profile. We solve the Jeans equations numerically for the model and explored the parameter space under the additional requirement that the model must predict the correct astrometry for the quasar images. Given the current error bars on f_b and sigma_ap, we did not constrain H0 yet with high accuracy, i.e., we found a broad range of models with chi^2 < 1. However, narrowing this range is possible, provided a better velocity dispersion measurement becomes available. In addition, increasing the depth of the current HST imaging data of HE 0435-1223 will allow us to combine our constraints with lens reconstruction techniques that make use of the full Einstein ring that is visible in this object.Comment: 12 pages, 10 figures, final version accepted for publication by A&

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Variation in the Analysis of Positively Selected Sites Using Nonsynonymous/Synonymous Rate Ratios: An Example Using Influenza Virus

Sites in a gene showing the nonsynonymous/synonymous rate ratio (ω) >1 have been frequently identified to be under positive selection. To examine the performance of such analysis, sites of the ω ratio >1 in the HA1 gene of H3N2 subtype human influenza viruses were identified from seven overlapping sequence data sets in this study. Our results showed that the sites of the ω ratio >1 were of significant variation among the data sets even though they targeted similar clusters, indicating that the analysis is likely to be either of low sensitivity or of low specificity in identifying sites under positive selection. Most (43/45) of the sites showing ω >1 calculated from at least one data set are involved in B-cell epitopes which cover less than a half sites in the protein, suggesting that the analysis is likely to be of low sensitivity rather than of low specificity. It was further found that the analysis sensitivity could not be enhanced by including more sequences or covering longer time intervals. Previously some reports also likely identified only a portion of the sites under positive selection in the viral gene using the ω ratio. Low sensitivity of the analysis may result from that some sites under positive selection in the gene are also under negative (purifying) selection simultaneously for functional constrains, and so their ω ratios could be <1. Theoretically, the sites under the two opposite selection forces at the same time favor only certain nonsynonymous changes, e.g. those changing the antigenicity of the gene and maintaining the gene function. This study also suggested that sometimes we can identify more sites under positive selection using the ω ratio by integrating the positively selected sites estimated from multiple data sets

Molecular characterization of partial-open reading frames 1a and 2 of the human astroviruses in South Korea

Human astroviruses (HAstVs) are among the major causes of gastroenteritis in South Korea. In this study, the partial regions of the open reading frame (ORF) 1a and ORF2 genes of HAstVs from gastroenteritis patients in nine hospitals were sequenced, and the molecular characterization of the viruses was revealed. 89 partial nucleotide sequences of ORF1a and 88 partial nucleotide sequences of ORF2 were amplified from 120 stool specimens. Phylogenetic analysis showed that most of the nucleotide sequences of ORF1a and ORF2 were grouped with HAstV type 1 but had evolutionary genetic distance compared with the reference sequences, such as the HAstV-1 prototype, Dresden strain, and Oxford strain. According to the phylogenetic analysis, some nucleotide sequences including SE0506041, SE0506043, and SE0506058, showed the discrepancy of the genotypes, but there was no proof of recombination among the HAstV types. In conclusion, this study showed that the dominant HAstV isolated from the Seoul metropolitan area in 2004-2005 was HAstV type 1, and that Korean HAstV-1 had the genetic distance in evolution compared with the reference sequences of HAstVs. Lots of nucleotide sequences of the ORF1a and ORF2 genes of HAstV will be useful for studying for the control and prevention of HAstV gastroenteritis in South Korea