The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes

Phylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.
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MC2^2: Subaru and Hubble Space Telescope Weak-Lensing Analysis of the Double Radio Relic Galaxy Cluster PLCK G287.0+32.9

The second most significant detection of the Planck Sunyaev Zel'dovich survey, PLCK~G287.0+32.9 ($z=0.385$) boasts two similarly bright radio relics and a radio halo. One radio relic is located $\sim 400$ kpc northwest of the X-ray peak and the other $\sim 2.8$ Mpc to the southeast. This large difference suggests that a complex merging scenario is required. A key missing puzzle for the merging scenario reconstruction is the underlying dark matter distribution in high resolution. We present a joint Subaru Telescope and {\it Hubble Space Telescope} weak-lensing analysis of the cluster. Our analysis shows that the mass distribution features four significant substructures. Of the substructures, a primary cluster of mass $M_{200\text{c}}=1.59^{+0.25}_{-0.22}\times 10^{15} \ h^{-1}_{70} \ \text{M}_{\odot}$dominates the weak-lensing signal. This cluster is likely to be undergoing a merger with one (or more) subcluster whose mass is approximately a factor of 10 lower. One candidate is the subcluster of mass$M_{200\text{c}}=1.16^{+0.15}_{-0.13}\times 10^{14} \ h^{-1}_{70} \ \text{M}_{\odot}$located$\sim 400$kpc to the southeast. The location of this subcluster suggests that its interaction with the primary cluster could be the source of the NW radio relic. Another subcluster is detected$\sim 2$Mpc to the SE of the X-ray peak with mass$M_{200\text{c}}=1.68^{+0.22}_{-0.20}\times 10^{14} \ h^{-1}_{70} \ \text{M}_{\odot}$. This SE subcluster is in the vicinity of the SE radio relic and may have created the SE radio relic during a past merger with the primary cluster. The fourth subcluster,$M_{200\text{c}}=1.87^{+0.24}_{-0.22}\times 10^{14} \ h^{-1}_{70} \ \text{M}_{\odot}$, is northwest of the X-ray peak and beyond the NW radio relic.Comment: 19 pages, 14 figures; Accepted to Ap

Stabilized Finite Elements in FUN3D

A Streamlined Upwind Petrov-Galerkin (SUPG) stabilized finite-element discretization has been implemented as a library into the FUN3D unstructured-grid flow solver. Motivation for the selection of this methodology is given, details of the implementation are provided, and the discretization for the interior scheme is verified for linear and quadratic elements by using the method of manufactured solutions. A methodology is also described for capturing shocks, and simulation results are compared to the finite-volume formulation that is currently the primary method employed for routine engineering applications. The finite-element methodology is demonstrated to be more accurate than the finite-volume technology, particularly on tetrahedral meshes where the solutions obtained using the finite-volume scheme can suffer from adverse effects caused by bias in the grid. Although no effort has been made to date to optimize computational efficiency, the finite-element scheme is competitive with the finite-volume scheme in terms of computer time to reach convergence

Wind-Reprocessed Transients from Stellar-mass Black Hole Tidal Disruption Events

Tidal disruptions of stars by stellar-mass black holes are expected to occur frequently in dense star clusters. Building upon previous studies that performed hydrodynamic simulations of these encounters, we explore the formation and long-term evolution of the thick, super-Eddington accretion disks formed. We build a disk model that includes fallback of material from the tidal disruption, accretion onto the black hole, and disk mass losses through winds launched in association with the super-Eddington flow. We demonstrate that bright transients are expected when radiation from the central engine powered by accretion onto the black hole is reprocessed at large radii by the optically-thick disk wind. By combining hydrodynamic simulations of these disruption events with our disk+wind model, we compute light curves of these wind-reprocessed transients for a wide range of stellar masses and encounter penetration depths. We find typical peak bolometric luminosities of roughly $10^{41}-10^{44}\,$erg/s (depending mostly on accretion physics parameters) and temperatures of roughly $10^5-10^6\,$K, suggesting peak emission in the ultraviolet/blue bands. We predict all-sky surveys such as the Vera Rubin Observatory and ULTRASAT will detect up to thousands of these events per year in dense star clusters out to distances of several Gpc.Comment: 16 Pages, 13 figures, 2 tables. Accepted for publication in MNRA

Preventing Supply Chain Vulnerabilities in Java with a Fine-Grained Permission Manager

Integrating third-party packages accelerates modern software engineering, but introduces the risk of software supply chain vulnerabilities. Vulnerabilities in applications' dependencies are being exploited worldwide. Often, these exploits leverage features that are present in a package, yet unneeded by an application. Unfortunately, the current generation of permission managers, such as SELinux, Docker containers, and the Java Security Manager, are too coarse-grained to usefully support engineers and operators in mitigating these vulnerabilities. Current approaches offer permissions only at the application's granularity, lumping legitimate operations made by safe packages with illegitimate operations made by exploited packages. This strategy does not reflect modern engineering practice. we need a permission manager capable of distinguishing between actions taken by different packages in an application's supply chain. In this paper, we describe Next-JSM, the first fine-grained ("supply chain aware") permission manager for Java applications. Next-JSM supports permission management at package-level granularity. Next-JSM faces three key challenges: operating on existing JVMs and without access to application or package source code, minimizing performance overhead in applications with many packages, and helping operators manage finer-grained permissions. We show that these challenges can be addressed through bytecode rewriting; appropriate data structures and algorithms; and an expressive permission notation plus automated tooling to establish default permission. In our evaluation, we report that Next-JSM mitigates 11 of the 12 package vulnerabilities we evaluated and incurs an average 2.72% overhead on the Dacapobench benchmark. Qualitatively, we argue that Next-JSM addresses the shortcomings of the (recently deprecated) Java Security Manager (JSM).Comment: 15 pages, 5 figures, 5 table

Basic Features of a Cell Electroporation Model: Illustrative Behavior for Two Very Different Pulses

Science increasingly involves complex modeling. Here we describe a model for cell electroporation in which membrane properties are dynamically modified by poration. Spatial scales range from cell membrane thickness (5 nm) to a typical mammalian cell radius (10 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}\upmu\end{document}m), and can be used with idealized and experimental pulse waveforms. The model consists of traditional passive components and additional active components representing nonequilibrium processes. Model responses include measurable quantities: transmembrane voltage, membrane electrical conductance, and solute transport rates and amounts for the representative “long” and “short” pulses. The long pulse—1.5 kV/cm, 100 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}\upmu\end{document}s—evolves two pore subpopulations with a valley at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\sim}$$\end{document}5 nm, which separates the subpopulations that have peaks at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\sim}$$\end{document}1.5 and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\sim}$$\end{document}12 nm radius. Such pulses are widely used in biological research, biotechnology, and medicine, including cancer therapy by drug delivery and nonthermal physical tumor ablation by causing necrosis. The short pulse—40 kV/cm, 10 ns—creates 80-fold more pores, all small (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$<$$\end{document}3 nm; \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim$$\end{document}1 nm peak). These nanosecond pulses ablate tumors by apoptosis. We demonstrate the model’s responses by illustrative electrical and poration behavior, and transport of calcein and propidium. We then identify extensions for expanding modeling capability. Structure-function results from MD can allow extrapolations that bring response specificity to cell membranes based on their lipid composition. After a pulse, changes in pore energy landscape can be included over seconds to minutes, by mechanisms such as cell swelling and pulse-induced chemical reactions that slowly alter pore behavior. Electronic supplementary material The online version of this article (doi:10.1007/s00232-014-9699-z) contains supplementary material, which is available to authorized users