Discriminating between a Stochastic Gravitational Wave Background and Instrument Noise

The detection of a stochastic background of gravitational waves could significantly impact our understanding of the physical processes that shaped the early Universe. The challenge lies in separating the cosmological signal from other stochastic processes such as instrument noise and astrophysical foregrounds. One approach is to build two or more detectors and cross correlate their output, thereby enhancing the common gravitational wave signal relative to the uncorrelated instrument noise. When only one detector is available, as will likely be the case with the Laser Interferometer Space Antenna (LISA), alternative analysis techniques must be developed. Here we show that models of the noise and signal transfer functions can be used to tease apart the gravitational and instrument noise contributions. We discuss the role of gravitational wave insensitive "null channels" formed from particular combinations of the time delay interferometry, and derive a new combination that maintains this insensitivity for unequal arm length detectors. We show that, in the absence of astrophysical foregrounds, LISA could detect signals with energy densities as low as $\Omega_{\rm gw} = 6 \times 10^{-13}$ with just one month of data. We describe an end-to-end Bayesian analysis pipeline that is able to search for, characterize and assign confidence levels for the detection of a stochastic gravitational wave background, and demonstrate the effectiveness of this approach using simulated data from the third round of Mock LISA Data Challenges.Comment: 10 Pages, 10 Figure

TI-Stan: Model comparison using thermodynamic integration and HMC

© 2019 by the authors. We present a novel implementation of the adaptively annealed thermodynamic integration technique using Hamiltonian Monte Carlo (HMC). Thermodynamic integration with importance sampling and adaptive annealing is an especially useful method for estimating model evidence for problems that use physics-based mathematical models. Because it is based on importance sampling, this method requires an efficient way to refresh the ensemble of samples. Existing successful implementations use binary slice sampling on the Hilbert curve to accomplish this task. This implementation works well if the model has few parameters or if it can be broken into separate parts with identical parameter priors that can be refreshed separately. However, for models that are not separable and have many parameters, a different method for refreshing the samples is needed. HMC, in the form of the MC-Stan package, is effective for jointly refreshing the ensemble under a high-dimensional model. MC-Stan uses automatic differentiation to compute the gradients of the likelihood that HMC requires in about the same amount of time as it computes the likelihood function itself, easing the programming burden compared to implementations of HMC that require explicitly specified gradient functions. We present a description of the overall TI-Stan procedure and results for representative example problems

The Woody Guthrie Centennial Bibliography

This bibliography updates two extensive works designed to include comprehensively all significant works by and about Woody Guthrie. Richard A. Reuss published A Woody Guthrie Bibliography, 1912–1967 in 1968 and Jeffrey N. Gatten\u27s article “Woody Guthrie: A Bibliographic Update, 1968–1986” appeared in 1988. With this current article, researchers need only utilize these three bibliographies to identify all English-language items of relevance related to, or written by, Guthrie

Organochlorine pesticides, PCBs, trace elements and metals in western pond turtle eggs from Oregon

With increased concern over the status of reptile populations globally, contaminant studies should be part of species evaluations. We analysed eggs of western pond turtles (Clemmys marmorata) from Fern Ridge Reservoir in western Oregon (USA) for 20 organochlorine (OC) pesticides or metabolites, 42 congener-specific polychlorinated biphenyls (PCBs), and 16 trace elements or metals. These eggs represent the first of this species analysed. The OC pesticides and PCB residue concentrations in the western pond turtle eggs were generally low and similar to those found in eggs of snapping turtles (Chelydra serpentina) from a remote site in Ontario, Canada. Western pond turtle eggs also contained mercury and chromium, which are metals of special concern. Although few reptilian eggs have been analysed for metals, the 44.9 micro g/g dry weight chromium in a western pond turtle egg in this study may be the highest reported in a reptilian egg. We found no significant difference in contaminant concentrations in eggs from nests in Oregon, where all turtle eggs failed to hatch compared to those where some eggs hatched. During this initial project, however, we were unable to assess fully the role of OCs, PCBs and other contaminants in the western pond turtle decline. Factors other than contaminants may be involved. In another study, snapping turtle eggs near the Great Lakes-St. Lawrence River basin were much more contaminated with evidence reported of effects on sex differentiation and reproductive endocrine function. Egg hatchability, the only reproductive parameter monitored, may not be the most sensitive endpoint. Other endpoints, including endocrine function, deformity rates, growth rates, and sex determination must be studied

A Population Phylogenetic View of Mitochondrial Heteroplasmy

The mitochondrion has recently emerged as an active player in myriad cellular processes. Additionally, it was recently shown that >200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model. Here, we present a population-genetic framework for modeling mitochondrial heteroplasmy as a process that occurs on an ontogenetic phylogeny, with genetic drift and mutation changing heteroplasmy frequencies during the various developmental processes represented in the phylogeny. Using this framework, we develop a Bayesian inference method for inferring rates of mitochondrial genetic drift and mutation at different stages of human life. Applying the method to previously published heteroplasmy frequency data, we demonstrate a severe effective germline bottleneck comprised of the cumulative genetic drift occurring between the divergence of germline and somatic cells in the mother, and the separation of germ layers in the offspring. Additionally, we find that the two somatic tissues we analyze here undergo tissue-specific bottlenecks during embryogenesis, less severe than the effective germline bottleneck, and that these somatic tissues experience little additional genetic drift during adulthood. We conclude with a discussion of possible extensions of the ontogenetic phylogeny framework and its possible applications to other ontogenetic processes in addition to mitochondrial heteroplasmy

Changes in retinoid metabolism and signaling associated with metabolic remodeling during fasting and in type I diabetes

Liver is the central metabolic hub that coordinates carbohydrate and lipid metabolism. The bioactive derivative of vitamin A, retinoic acid (RA), was shown to regulate major metabolic genes including phosphoenolpyruvate carboxykinase, fatty acid synthase, carnitine palmitoyltransferase 1, and glucokinase among others. Expression levels of these genes undergo profound changes during adaptation to fasting or in metabolic diseases such as type 1 diabetes (T1D). However, it is unknown whether the levels of hepatic RA change during metabolic remodeling. This study investigated the dynamics of hepatic retinoid metabolism and signaling in the fed state, in fasting, and in T1D. Our results show that fed-to-fasted transition is associated with significant decrease in hepatic retinol dehydrogenase (RDH) activity, the rate-limiting step in RA biosynthesis, and downregulation of RA signaling. The decrease in RDH activity correlates with the decreased abundance and altered subcellular distribution of RDH10 while Rdh10 transcript levels remain unchanged. In contrast to fasting, untreated T1D is associated with upregulation of RA signaling and an increase in hepatic RDH activity, which correlates with the increased abundance of RDH10 in microsomal membranes. The dynamic changes in RDH10 protein levels in the absence of changes in its transcript levels imply the existence of posttranscriptional regulation of RDH10 protein. Together, these data suggest that the downregulation of hepatic RA biosynthesis, in part via the decrease in RDH10, is an integral component of adaptation to fasting. In contrast, the upregulation of hepatic RA biosynthesis and signaling in T1D might contribute to metabolic inflexibility associated with this disease