The Panchromatic Hubble Andromeda Treasury XV. The BEAST: Bayesian Extinction and Stellar Tool

We present the Bayesian Extinction And Stellar Tool (BEAST), a probabilistic approach to modeling the dust extinguished photometric spectral energy distribution of an individual star while accounting for observational uncertainties common to large resolved star surveys. Given a set of photometric measurements and an observational uncertainty model, the BEAST infers the physical properties of the stellar source using stellar evolution and atmosphere models and constrains the line of sight extinction using a newly developed mixture model that encompasses the full range of dust extinction curves seen in the Local Group. The BEAST is specifically formulated for use with large multi-band surveys of resolved stellar populations. Our approach accounts for measurement uncertainties and any covariance between them due to stellar crowding (both systematic biases and uncertainties in the bias) and absolute flux calibration, thereby incorporating the full information content of the measurement. We illustrate the accuracy and precision possible with the BEAST using data from the Panchromatic Hubble Andromeda Treasury. While the BEAST has been developed for this survey, it can be easily applied to similar existing and planned resolved star surveys.Comment: 20 pages, 19 figures, ApJ, in pres

BEAST: Bayesian evolutionary analysis by sampling trees

<p>Abstract</p> <p>Background</p> <p>The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.</p> <p>Results</p> <p>BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at <url>http://beast-mcmc.googlecode.com/</url> under the GNU LGPL license.</p> <p>Conclusion</p> <p>BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.</p

πBUSS:a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies. Results: We present a flexible Monte Carlo simulation tool, called piBUSS, that employs the BEAGLE high performance library for phylogenetic computations within BEAST to rapidly generate large sequence alignments under complex evolutionary models. piBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. Analogous to BEAST model and analysis setup, more advanced simulation options are supported through an extensible markup language (XML) specification, which in addition to generating sequence output, also allows users to combine simulation and analysis in a single BEAST run. Conclusions: piBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, piBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. The software aims at implementing new models and data types that are continuously being developed as part of BEAST/BEAGLE.Comment: 13 pages, 2 figures, 1 tabl

The beast initiate: the lycanthropy of Heracles

The obscurantist Hellenistic poet Lycophron referenced the initiation of Heracles as a beast suckling the breast of the goddess Hera. This was the event that was the mythological origin of the Galaxy and of the lily flower that incarnated the same deifying essence as the celestial milk of the goddess and it was the etiology for the domestication of felines. As the Lion of Nemea, Heracles was the greatest of the wild cats. The lily was an analogue of a sacred mushroom, as the narkissos of Persephone’s abduction by Hades. The event of the lactation of Heracles is depicted on four Etruscan mirrors and a Faliscan-Hellenic red-figure krater. The deifying milk-flower of the goddess was a ritual of adoption into the family of the celestial deities, that Hera performed also with two other bastard sons of Zeus, Hermes and Dionysus. As the beast being initiated, Heracles became a wolf. Like the motif of the domestication of the cat, the lycanthropy of Heracles involves the whole family of canines, from the domesticated dog to its wilder antecedents in the wolf and its analogue as the fox. The lycanthropy initiation is a bacchanalian rite of root- cutters and is a motif of warrior brotherhood widespread among the Indo-European peoples.Published versio

BBCA: Improving the Scalability of *BEAST Using Random Binning

Species tree estimation can be challenging in the presence of gene tree conflict due to incomplete lineage sorting (ILS), which can occur when the time between speciation events is short relative to the population size. Of the many methods that have been developed to estimate species trees in the presence of ILS, *BEAST, a Bayesian method that co-estimates the species tree and gene trees given sequence alignments on multiple loci, has generally been shown to have the best accuracy. However, *BEAST is extremely computationally intensive so that it cannot be used with large numbers of loci; hence, *BEAST is not suitable for genome-scale analyses. Results: We present BBCA (boosted binned coalescent-based analysis), a method that can be used with *BEAST (and other such co-estimation methods) to improve scalability. BBCA partitions the loci randomly into subsets, uses *BEAST on each subset to co-estimate the gene trees and species tree for the subset, and then combines the newly estimated gene trees together using MP-EST, a popular coalescent-based summary method. We compare time-restricted versions of BBCA and *BEAST on simulated datasets, and show that BBCA is at least as accurate as *BEAST, and achieves better convergence rates for large numbers of loci. Conclusions: Phylogenomic analysis using *BEAST is currently limited to datasets with a small number of loci, and analyses with even just 100 loci can be computationally challenging. BBCA uses a very simple divide-and-conquer approach that makes it possible to use *BEAST on datasets containing hundreds of loci. This study shows that BBCA provides excellent accuracy and is highly scalable.Grant Agency of the Czech Republic P501-10-0208Academy of Sciences of the Czech Republic AVOZ50040507, AVOZ50040702, MSMT LC0604Ministry of Innovation and Science of Spain, MICINN CGL2007-64839-C02/BOSCSIC (Superior Council of Scientific InvestigationsJosé Castillejo Grant from the MICINN of the Spanish GovernmentComputer Science

Effects of creatine monohydrate supplementation on simulated soccer performance

Purpose: To determine the effects of acute short-term creatine (Cr) supplementation on physical performance during a 90-min soccer-specific performance test. Methods: A double-blind, placebo-controlled experimental design was adopted during which 16 male amateur soccer players were required to consume 20 g/d Cr for 7 d or a placebo. A Ball-Sport Endurance and Speed Test (BEAST) comprising measures of aerobic (circuit time), speed (12- and 20-m sprint), and explosive-power (vertical jump) abilities performed over 90 min was performed presupplementation and postsupplementation. Results: Performance measures during the BEAST deteriorated during the second half relative to the first for both Cr (1.2–2.3%) and placebo (1.0–2.2%) groups, indicating a fatigue effect associated with the BEAST. However, no significant differences existed between groups, suggesting that Cr had no performance-enhancing effect or ability to offset fatigue. When effect sizes were considered, some measures (12-m sprint, –0.53 ± 0.69; 20-m sprint, –0.39 ± 0.59) showed a negative tendency, indicating chances of harm were greater than chances of benefit. Conclusions: Acute short-term Cr supplementation has no beneficial effect on physical measures obtained during a 90-min soccer-simulation test, thus bringing into question its potential as an effective ergogenic aid for soccer players

Calibration and Irradiation Study of the BGO Background Monitor for the BEAST II Experiment

Beam commissioning of the SuperKEKB collider began in 2016. The Beam Exorcism for A STable experiment II (BEAST II) project is particularly designed to measure the beam backgrounds around the interaction point of the SuperKEKB collider for the Belle II experiment. We develop a system using bismuth germanium oxide (BGO) crystals with optical fibers connecting to a multianode photomultiplier tube (MAPMT) and a field-programmable gate array (FPGA) embedded readout board for monitoring the real-time beam backgrounds in BEAST II. The overall radiation sensitivity of this system is estimated to be $(2.20\pm0.26)\times10^{-12}$ Gy/ADU (analog-to-digital unit) with the standard 10 m fibers for transmission and the MAPMT operating at 700 V. Our $\gamma$-ray irradiation study of the BGO system shows that the exposure of BGO crystals to $^{60}$Co $\gamma$-ray doses of 1 krad has led to immediate light output reductions of 25--40%, and the light outputs further drop by 30--45% after the crystals receive doses of 2--4 krad. Our findings agree with those of the previous studies on the radiation hard (RH) BGO crystals grown by the low thermal gradient Czochralski (LTG Cz) technology. The absolute dose from the BGO system is also consistent with the simulation, and is estimated to be about 1.18 times the equivalent dose. These results prove that the BGO system is able to monitor the background dose rate in real time under extreme high radiation conditions. This study concludes that the BGO system is reliable for the beam background study in BEAST II

Victorian Influence on \u3cem\u3eBeauty and the Beast\u3c/em\u3e

This essay examines a unique publication of the well-known Beauty and the Beast fairy tale. W.B. Conkey Company’s adaptation of Beauty and the Beast demonstrates the influence of Victorian culture on children’s literature (1897). An in-depth analysis of the cultural and historical context of the publication uncovers new meaning in the lost text. This three-part analysis discusses norms of Victorian courtship, explains Victorian literary elements, and applies these cultural contexts to textual analysis. This lens highlights W.B. Conkey Company’s tailored message to a young Victorian audience