Joint estimation of multiple related biological networks

Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to share features. Here we present a hierarchical Bayesian formulation for joint estimation of multiple networks in this nonidentically distributed setting. The approach is general: given a suitable class of graphical models, it uses an exchangeability assumption on networks to provide a corresponding joint formulation. Motivated by emerging experimental designs in molecular biology, we focus on time-course data with interventions, using dynamic Bayesian networks as the graphical models. We introduce a computationally efficient, deterministic algorithm for exact joint inference in this setting. We provide an upper bound on the gains that joint estimation offers relative to separate estimation for each network and empirical results that support and extend the theory, including an extensive simulation study and an application to proteomic data from human cancer cell lines. Finally, we describe approximations that are still more computationally efficient than the exact algorithm and that also demonstrate good empirical performance.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS761 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Metal plasma immersion ion implantation and deposition using polymer substrates

This thesis investigates the application of plasma immersion ion implantation (PIII) to polymers. PIII requires that a high negative potential be applied to the surface of the material while it is immersed in a plasma. This presents a problem for insulating materials such as polymers, since the implanting ions carry charge to the surface, resulting in a charge accumulation that effectively neutralises the applied potential. This causes the plasma sheath at the surface to collapse a short time after the potential is applied. Measurements of the sheath dynamics, including the collapsing sheath, are performed using an electric probe. The results are compared to theoretical models of the plasma sheath based on the Child-Langmuir law for high voltage sheaths. The theoretical model predicts well the sheath dynamics for conductive substrates. For insulating substrates the model can account for the experimental observations if the secondary electron coefficient is modified, justified on the basis of the poly-energetic nature of the implanting ions. If a conductive film is applied to the insulator surface the problem of charge accumulation can be avoided without compromising the effectiveness of PIII. The requirement for the film is that it be conductive, yet transparent to the incident ions. Experimental results are presented which confirm the effectiveness of the method. Theoretical estimates of the surface potential show that a film of the order of 5nm thickness can effectively circumvent the charge accumulation problem. Efforts to produce and characterise such a film form the final two chapters of this thesis. The optimal thickness is determined to be near the percolation threshold, where a marked increase in conductivity occurs. Spectroscopic ellipsometry is shown to be an excellent method to determine the film thickness and percolation threshold non-invasively. Throughout this work cathodic vacuum arcs are used to deposit thin films and as a source of metal plasmas. The design and construction of a pulsed cathodic vacuum arc forms a significant part of this thesis. Investigations of the cathode spots and power supply requirements are presented

GRB Flares: UV/Optical Flaring (Paper I)

We present a new algorithm for the detection of flares in gamma-ray burst (GRB) light curves and use this algorithm to detect flares in the UV/optical. The algorithm makes use of the Bayesian Information Criterion (BIC) to analyze the residuals of the fitted light curve, removing all major features, and to determine the statistically best fit to the data by iteratively adding additional `breaks' to the light curve. These additional breaks represent the individual components of the detected flares: T_start, T_stop, and T_peak. We present the detection of 119 unique flaring periods detected by applying this algorithm to light curves taken from the Second Swift Ultraviolet/Optical Telescope (UVOT) GRB Afterglow Catalog. We analyzed 201 UVOT GRB light curves and found episodes of flaring in 68 of the light curves. For those light curves with flares, we find an average number of ~2 flares per GRB. Flaring is generally restricted to the first 1000 seconds of the afterglow, but can be observed and detected beyond 10^5 seconds. More than 80% of the flares detected are short in duration with Delta t/t of < 0.5. Flares were observed with flux ratios relative to the underlying light curve of between 0.04 to 55.42. Many of the strongest flares were also seen at greater than 1000 seconds after the burst.Comment: Submitted to ApJ. 20 pages (including 8 figures and 1 table

High accuracy measure of atomic polarizability in an optical lattice clock

Despite being a canonical example of quantum mechanical perturbation theory, as well as one of the earliest observed spectroscopic shifts, the Stark effect contributes the largest source of uncertainty in a modern optical atomic clock through blackbody radiation. By employing an ultracold, trapped atomic ensemble and high stability optical clock, we characterize the quadratic Stark effect with unprecedented precision. We report the ytterbium optical clock's sensitivity to electric fields (such as blackbody radiation) as the differential static polarizability of the ground and excited clock levels: 36.2612(7) kHz (kV/cm)^{-2}. The clock's fractional uncertainty due to room temperature blackbody radiation is reduced an order of magnitude to 3 \times 10^{-17}.Comment: 5 pages, 3 figures, 2 table

NODULAR MASSES IN THE SWIMBLADDER AND VISCERAL FAT OF THE WALLEYE, \u3ci\u3eSTIZOSTEDION VITREUM\u3c/i\u3e

In April of 1990, a 1.8 kg walleye was found to contain hard cysts or nodules in the swimbladder and visceral fat. The nodules appeared to be formed around a worm-like mass. The nodules (10 ± 5 mm in diameter) were composed of five to seven layers of tightly packed granules, that were at least partially calcified and the layers were held together by a sticky matrix. The outer coat of the nodule was convoluted with many protuberances. This is a first report of such cysts from fish and they appear to be similar to nodules induced by worms (encysted nematodes) in the intestines of swine and ruminants

BLOOD AND TISSUE IDENTIFICATION OF SELECTED BIRDS AND MAMMALS, PART II: Cross Reaction Patterns of Birds and Mammals, Using Deer, Bovine, Raccoon, Chicken and Mallard Duck Antiserum, part 4

Part 4 (pp. 86-114) Mammals (Figure 10), continued Horse Human Mink Opossum Pig Porcupine. Prairie Dog Raccoon Big Horn Sheep Domestic Sheep Striped Skunk Fox Squirrel Discussio

Frequency evaluation of the doubly forbidden 1S0→3P0^1S_0\to ^3P_0 transition in bosonic 174^{174}Yb

We report an uncertainty evaluation of an optical lattice clock based on the $^1S_0\leftrightarrow^3P_0$ transition in the bosonic isotope $^{174}$Yb by use of magnetically induced spectroscopy. The absolute frequency of the $^1S_0\leftrightarrow^3P_0$ transition has been determined through comparisons with optical and microwave standards at NIST. The weighted mean of the evaluations is $\nu$($^{174}$Yb)=518 294 025 309 217.8(0.9) Hz. The uncertainty due to systematic effects has been reduced to less than 0.8 Hz, which represents $1.5\times10^{-15}$ in fractional frequency.Comment: 4 pages, 3 figure -Submitted to PRA Rapid Communication