Model of Transcriptional Activation by MarA in Escherichia coli

We have developed a mathematical model of transcriptional activation by MarA in Escherichia coli, and used the model to analyze measurements of MarA-dependent activity of the marRAB, sodA, and micF promoters in mar-rob- cells. The model rationalizes an unexpected poor correlation between the mid-point of in vivo promoter activity profiles and in vitro equilibrium constants for MarA binding to promoter sequences. Analysis of the promoter activity data using the model yielded the following predictions regarding activation mechanisms: (1) MarA activation of the marRAB, sodA, and micF promoters involves a net acceleration of the kinetics of transitions after RNA polymerase binding, up to and including promoter escape and message elongation; (2) RNA polymerase binds to these promoters with nearly unit occupancy in the absence of MarA, making recruitment of polymerase an insignificant factor in activation of these promoters; and (3) instead of recruitment, activation of the micF promoter might involve a repulsion of polymerase combined with a large acceleration of the kinetics of polymerase activity. These predictions are consistent with published chromatin immunoprecipitation assays of interactions between polymerase and the E. coli chromosome. A lack of recruitment in transcriptional activation represents an exception to the textbook description of activation of bacterial sigma-70 promoters. However, use of accelerated polymerase kinetics instead of recruitment might confer a competitive advantage to E. coli by decreasing latency in gene regulation.Comment: 30 pages, 2 figure

Gravitational Wave Burst Source Direction Estimation using Time and Amplitude Information

In this article we study two problems that arise when using timing and amplitude estimates from a network of interferometers (IFOs) to evaluate the direction of an incident gravitational wave burst (GWB). First, we discuss an angular bias in the least squares timing-based approach that becomes increasingly relevant for moderate to low signal-to-noise ratios. We show how estimates of the arrival time uncertainties in each detector can be used to correct this bias. We also introduce a stand alone parameter estimation algorithm that can improve the arrival time estimation and provide root-sum-squared strain amplitude (hrss) values for each site. In the second part of the paper we discuss how to resolve the directional ambiguity that arises from observations in three non co-located interferometers between the true source location and its mirror image across the plane containing the detectors. We introduce a new, exact relationship among the hrss values at the three sites that, for sufficiently large signal amplitudes, determines the true source direction regardless of whether or not the signal is linearly polarized. Both the algorithm estimating arrival times, arrival time uncertainties, and hrss values and the directional follow-up can be applied to any set of gravitational wave candidates observed in a network of three non co-located interferometers. As a case study we test the methods on simulated waveforms embedded in simulations of the noise of the LIGO and Virgo detectors at design sensitivity.Comment: 10 pages, 14 figures, submitted to PR

The Energy-dependent X-ray Timing Characteristics of the Narrow Line Seyfert 1 Mkn 766

We present the energy-dependent power spectral density (PSD) and cross-spectral properties of Mkn 766, obtained from combining data obtained during an XMM-Newton observation spanning six revolutions in 2005 with data obtained from an XMM-Newton long-look in 2001. The PSD shapes and rms-flux relations are found to be consistent between the 2001 and 2005 observations, suggesting the 2005 observation is simply a low-flux extension of the 2001 observation and permitting us to combine the two data sets. The resulting PSD has the highest temporal frequency resolution for any AGN PSD measured to date. Applying a broken power-law model yields break frequencies which increase in temporal frequency with photon energy. Obtaining a good fit when assuming energy-independent break frequencies requires the presence of a Lorentzian at 4.6+/-0.4 * 10^-4 Hz whose strength increases with photon energy, a behavior seen in black hole X-ray binaries. The cross-spectral properties are measured; temporal frequency-dependent soft-to-hard time lags are detected in this object for the first time. Cross-spectral results are consistent with those for other accreting black hole systems. The results are discussed in the context of several variability models, including those based on inwardly-propagating viscosity variations in the accretion disk.Comment: Accepted for publication in The Astrophysical Journal. 18 pages, 9 figures. Uses emulateapj5.st

Spatial and seasonal relationships between Pacific harbor seals (Phoca vitulina richardii) and their prey, at multiple scales

Knowing where pinnipeds forage is vital to managing and protecting their populations, and for assessing potential interactions with fisheries. We assessed the spatial relationship between the seasonal distribution of Pacific harbor seals (Phoca vitulina richardii) outfitted with satellite transmitters and the seasonal distributions of potential harbor seal prey species in San Francisco Bay, California. Pearson’s correlation coefficients were calculated between the number of harbor seal locations in an area of the San Francisco Bay and the abundance of specific prey species in the same area. The influence of scale on the analyses was assessed by varying the scale of analysis from 1 to 10 km. There was consistency in the prey species targeted by harbor seals year-round, although there were seasonal differences between the most important prey species. The highest correlations between harbor seals and their prey were found for seasonally abundant benthic species, located within about 10 km of the primary haul-out site. Probable foraging habitat for harbor seals was identified, based on areas with high abundances of prey species that were strongly correlated with harbor seal distribution. With comparable local data inputs, this approach has potential application to pinniped management in other areas, and to decisions about the location of marine reserves designed to protect these species

Random Matrix Theory Analysis of Cross Correlations in Financial Markets

We confirm universal behaviors such as eigenvalue distribution and spacings predicted by Random Matrix Theory (RMT) for the cross correlation matrix of the daily stock prices of Tokyo Stock Exchange from 1993 to 2001, which have been reported for New York Stock Exchange in previous studies. It is shown that the random part of the eigenvalue distribution of the cross correlation matrix is stable even when deterministic correlations are present. Some deviations in the small eigenvalue statistics outside the bounds of the universality class of RMT are not completely explained with the deterministic correlations as proposed in previous studies. We study the effect of randomness on deterministic correlations and find that randomness causes a repulsion between deterministic eigenvalues and the random eigenvalues. This is interpreted as a reminiscent of ``level repulsion'' in RMT and explains some deviations from the previous studies observed in the market data. We also study correlated groups of issues in these markets and propose a refined method to identify correlated groups based on RMT. Some characteristic differences between properties of Tokyo Stock Exchange and New York Stock Exchange are found.Comment: RevTex, 17 pages, 8 figure

Managing Risk of Bidding in Display Advertising

In this paper, we deal with the uncertainty of bidding for display advertising. Similar to the financial market trading, real-time bidding (RTB) based display advertising employs an auction mechanism to automate the impression level media buying; and running a campaign is no different than an investment of acquiring new customers in return for obtaining additional converted sales. Thus, how to optimally bid on an ad impression to drive the profit and return-on-investment becomes essential. However, the large randomness of the user behaviors and the cost uncertainty caused by the auction competition may result in a significant risk from the campaign performance estimation. In this paper, we explicitly model the uncertainty of user click-through rate estimation and auction competition to capture the risk. We borrow an idea from finance and derive the value at risk for each ad display opportunity. Our formulation results in two risk-aware bidding strategies that penalize risky ad impressions and focus more on the ones with higher expected return and lower risk. The empirical study on real-world data demonstrates the effectiveness of our proposed risk-aware bidding strategies: yielding profit gains of 15.4% in offline experiments and up to 17.5% in an online A/B test on a commercial RTB platform over the widely applied bidding strategies

The Suzaku Observation of NGC 3516: Complex Absorption and the Broad and Narrow Fe K Lines

We present results from a 150 ksec Suzaku observation of the Seyfert 1.5 NGC 3516 in October 2005. The source was in a relatively highly absorbed state. Our best-fit model is consistent with the presence of a low-ionization absorber which has a column density near 5 * 10^{22} cm^{-2} and covers most of the X-ray continuum source (covering fraction 96-100%). A high-ionization absorbing component, which yields a narrow absorption feature consistent with Fe K XXVI, is confirmed. A relativistically broadened Fe K alpha line is required in all fits, even after the complex absorption is taken into account; an additional partial-covering component is an inadequate substitute for the continuum curvature associated with the broad Fe line. A narrow Fe K alpha emission line has a velocity width consistent with the Broad Line Region. The low-ionization absorber may be responsible for producing the narrow Fe K alpha line, though a contribution from additional material out of the line of sight is possible. We include in our model soft band emission lines from He- and H-like ions of N, O, Ne and Mg, consistent with photo-ionization, though a small contribution from collisionally-ionized emission is possible.Comment: Accepted for publication in PASJ (Suzaku second special issue). 36 pages, 10 figure

Connection between the Accretion Disk and Jet in the Radio Galaxy 3C 111

We present the results of extensive multi-frequency monitoring of the radio galaxy 3C 111 between 2004 and 2010 at X-ray (2.4--10 keV), optical (R band), and radio (14.5, 37, and 230 GHz) wave bands, as well as multi-epoch imaging with the Very Long Baseline Array (VLBA) at 43 GHz. Over the six years of observation, significant dips in the X-ray light curve are followed by ejections of bright superluminal knots in the VLBA images. This shows a clear connection between the radiative state near the black hole, where the X-rays are produced, and events in the jet. The X-ray continuum flux and Fe line intensity are strongly correlated, with a time lag shorter than 90 days and consistent with zero. This implies that the Fe line is generated within 90 light-days of the source of the X-ray continuum. The power spectral density function of X-ray variations contains a break, with steeper slope at shorter timescales. The break timescale of 13 (+12,-6) days is commensurate with scaling according to the mass of the central black hole based on observations of Seyfert galaxies and black hole X-ray binaries (BHXRBs). The data are consistent with the standard paradigm, in which the X-rays are predominantly produced by inverse Compton scattering of thermal optical/UV seed photons from the accretion disk by a distribution of hot electrons --- the corona --- situated near the disk. Most of the optical emission is generated in the accretion disk due to reprocessing of the X-ray emission. The relationships that we have uncovered between the accretion disk and the jet in 3C 111, as well as in the FR I radio galaxy 3C 120 in a previous paper, support the paradigm that active galactic nuclei and Galactic BHXRBs are fundamentally similar, with characteristic time and size scales proportional to the mass of the central black holeComment: Accepted for publication in ApJ. 18 pages, 17 figures, 11 tables (full machine readable data-tables online in ApJ website

Adaptive Investment Strategies For Periodic Environments

In this paper, we present an adaptive investment strategy for environments with periodic returns on investment. In our approach, we consider an investment model where the agent decides at every time step the proportion of wealth to invest in a risky asset, keeping the rest of the budget in a risk-free asset. Every investment is evaluated in the market via a stylized return on investment function (RoI), which is modeled by a stochastic process with unknown periodicities and levels of noise. For comparison reasons, we present two reference strategies which represent the case of agents with zero-knowledge and complete-knowledge of the dynamics of the returns. We consider also an investment strategy based on technical analysis to forecast the next return by fitting a trend line to previous received returns. To account for the performance of the different strategies, we perform some computer experiments to calculate the average budget that can be obtained with them over a certain number of time steps. To assure for fair comparisons, we first tune the parameters of each strategy. Afterwards, we compare the performance of these strategies for RoIs with different periodicities and levels of noise.Comment: Paper submitted to Advances in Complex Systems (November, 2007) 22 pages, 9 figure