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

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

Costs of Collective Decisions, Choice of Tax Base, and Median Voter Equilibrium

This note examines the relationship between public expenditure growth and tax base elasticity in the context of the median voter model. If the revenue elasticity of the tax base and the median voter's income elasticity of demand for public services are not identical, the automatic increase in public revenue resulting from an increase in voter income will not match the median voter's increase in demand for public service expenditures. If adjusting tax rates is costly, the short-run rate of growth ofpublic expenditures will be biased in the direction of the automatic growth in tax revenue rather than being tied directly to changes in the median voter's demand for public services. The welfare loss occasioned by these positive decision-making costs can be reduced by choosing that tax base for which revenue elasticity most closely corresponds to income elasticity and also by evaluating tax rates in a multiperiod context at the time they are imposed.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

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

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

Quenched Narrow-Line Laser Cooling of 40Ca to Near the Photon Recoil Limit

We present a cooling method that should be generally applicable to atoms with narrow optical transitions. This technique uses velocity-selective pulses to drive atoms towards a zero-velocity dark state and then quenches the excited state to increase the cooling rate. We demonstrate this technique of quenched narrow-line cooling by reducing the 1-D temperature of a sample of neutral 40Ca atoms. We velocity select and cool with the 1S0(4s2) to 3P1(4s4p) 657 nm intercombination line and quench with the 3P1(4s4p) to 1S0(4s5s) intercombination line at 553 nm, which increases the cooling rate eight-fold. Limited only by available quenching laser power, we have transferred 18 % of the atoms from our initial 2 mK velocity distribution and achieved temperatures as low as 4 microK, corresponding to a vrms of 2.8 cm/s or 2 recoils at 657 nm. This cooling technique, which is closely related to Raman cooling, can be extended to three dimensions.Comment: 5 pages, 4 figures; Submitted to PRA Rapid Communication

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

Measurement of excited-state transitions in cold calcium atoms by direct femtosecond frequency-comb spectroscopy

We apply direct frequency-comb spectroscopy, in combination with precision cw spectroscopy, to measure the ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency in cold calcium atoms. A 657 nm ultrastable cw laser was used to excite atoms on the narrow ($\gamma \sim 400$ Hz) ${\rm 4s^2} ^1S_0 \to {\rm 4s4p} ^3P_1$ clock transition, and the direct output of the frequency comb was used to excite those atoms from the ${\rm 4s4p} ^3P_1$ state to the ${\rm 4s5s} ^3S_1$ state. The resonance of this second stage was detected by observing a decrease in population of the ground state as a result of atoms being optically pumped to the metastable ${\rm 4s4p} ^3P_{0,2}$ states. The ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency is measured to be $\nu = 489 544 285 713(56)$ kHz; which is an improvement by almost four orders of magnitude over the previously measured value. In addition, we demonstrate spectroscopy on magnetically trapped atoms in the ${\rm 4s4p} ^3P_2$ state.Comment: 4 pages 5 figure