Bang the Can Slowly: An Investigation into the 2017 Houston Astros

This manuscript is a statistical investigation into the 2017 Major League Baseball scandal involving the Houston Astros, the World Series championship winner that same year. The Astros were alleged to have stolen their opponents' pitching signs in order to provide their batters with a potentially unfair advantage. This work finds compelling evidence that the Astros on-field performance was significantly affected by their sign-stealing ploy and quantifies the effects. The three main findings in the manuscript are: 1) the Astros' odds of swinging at a pitch were reduced by approximately 27% (OR: 0.725, 95% CI: (0.618, 0.850)) when the sign was stolen, 2) when an Astros player swung, the odds of making contact with the ball increased roughly 80% (OR: 1.805, 95% CI: (1.342, 2.675)) on non-fastball pitches, and 3) when the Astros made contact with a ball on a pitch in which the sign was known, the ball's exit velocity (launch speed) increased on average by 2.386 (95% CI: (0.334, 4.451)) miles per hour

Understanding natural selection: essential concepts and common misconceptions

Abstract Natural selection is one of the central mechanisms of evolutionary change and is the process responsible for the evolution of adaptive features. Without a working knowledge of natural selection, it is impossible to understand how or why living things have come to exhibit their diversity and complexity. An understanding of natural selection also is becoming increasingly relevant in practical contexts, including medicine, agriculture, and resource management. Unfortunately, studies indicate that natural selection is generally very poorly understood, even among many individuals with postsecondary biological education. This paper provides an overview of the basic process of natural selection, discusses the extent and possible causes of misunderstandings of the process, and presents a review of the most common misconceptions that must be corrected before a functional understanding of natural selection and adaptive evolution can be achieved

The dynamic evolutionary history of genome size in North American woodland salamanders

© 2017 Published by NRC Research Press. The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders

T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis

<p>Abstract</p> <p>Background</p> <p>T4 RNA ligases 1 and 2 are useful tools for RNA analysis. Their use upstream of RNA analyses such as high-throughput RNA sequencing and microarrays has recently increased their importance. The truncated form of T4 RNA ligase 2, comprising amino acids 1-249 (T4 Rnl2tr), is an attractive tool for attachment of adapters or labels to RNA 3'-ends. Compared to T4 RNA ligase 1, T4 Rnl2tr has a decreased ability to ligate 5'-PO₄ends in single-stranded RNA ligations, and compared to the full-length T4 Rnl2, the T4 Rnl2tr has an increased activity for joining 5'-adenylated adapters to RNA 3'-ends. The combination of these properties allows adapter attachment to RNA 3'-ends with reduced circularization and concatemerization of substrate RNA.</p> <p>Results</p> <p>With the aim of further reducing unwanted side ligation products, we substituted active site residues, known to be important for adenylyltransferase steps of the ligation reaction, in the context of T4 Rnl2tr. We characterized the variant ligases for the formation of unwanted ligation side products and for activity in the strand-joining reaction.</p> <p>Conclusions</p> <p>Our data demonstrate that lysine 227 is a key residue facilitating adenylyl transfer from adenylated ligation donor substrates to the ligase. This reversal of the second step of the ligation reaction correlates with the formation of unwanted ligation products. Thus, T4 Rn2tr mutants containing the K227Q mutation are useful for reducing undesired ligation products. We furthermore report optimal conditions for the use of these improved T4 Rnl2tr variants.</p

CASTER - a concept for a Black Hole Finder Probe based on the use of new scintillator technologies

The primary scientific mission of the Black Hole Finder Probe (BHFP), part of the NASA Beyond Einstein program, is to survey the local Universe for black holes over a wide range of mass and accretion rate. One approach to such a survey is a hard X-ray coded-aperture imaging mission operating in the 10--600 keV energy band, a spectral range that is considered to be especially useful in the detection of black hole sources. The development of new inorganic scintillator materials provides improved performance (for example, with regards to energy resolution and timing) that is well suited to the BHFP science requirements. Detection planes formed with these materials coupled with a new generation of readout devices represent a major advancement in the performance capabilities of scintillator-based gamma cameras. Here, we discuss the Coded Aperture Survey Telescope for Energetic Radiation (CASTER), a concept that represents a BHFP based on the use of the latest scintillator technology.Comment: 12 pages; conference paper presented at the SPIE conference "UV, X-Ray, and Gamma-Ray Space Instrumentation for Astronomy XIV." To be published in SPIE Conference Proceedings, vol. 589

Distinguishing ecological from evolutionary approaches to transposable elements

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology

EVALUATING ARTIFICIAL INTELLIGENCE METHODS FOR USE IN KILL CHAIN FUNCTIONS

Current naval operations require sailors to make time-critical and high-stakes decisions based on uncertain situational knowledge in dynamic operational environments. Recent tragic events have resulted in unnecessary casualties, and they represent the decision complexity involved in naval operations and specifically highlight challenges within the OODA loop (Observe, Orient, Decide, and Assess). Kill chain decisions involving the use of weapon systems are a particularly stressing category within the OODA loop—with unexpected threats that are difficult to identify with certainty, shortened decision reaction times, and lethal consequences. An effective kill chain requires the proper setup and employment of shipboard sensors; the identification and classification of unknown contacts; the analysis of contact intentions based on kinematics and intelligence; an awareness of the environment; and decision analysis and resource selection. This project explored the use of automation and artificial intelligence (AI) to improve naval kill chain decisions. The team studied naval kill chain functions and developed specific evaluation criteria for each function for determining the efficacy of specific AI methods. The team identified and studied AI methods and applied the evaluation criteria to map specific AI methods to specific kill chain functions.Civilian, Department of the NavyCivilian, Department of the NavyCivilian, Department of the NavyCaptain, United States Marine CorpsCivilian, Department of the NavyCivilian, Department of the NavyApproved for public release. Distribution is unlimited