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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Judicial Antagonism to Executive Power: An Analysis of Emerging Doctrinal Trends in Federal Courts

Kyle James is a senior Political Science major at Seton Hall University and the Executive Editor of Political Analysis. Following graduation, he will be attending Wake Forest University School of Law as a JD candidate. He aspires to practice securities, antitrust, and regulatory law in Washington D.C. or North Carolina. His research interests include federal courts, civil procedure, and administrative law. This paper was conceived in response to recent judicial decisions that have upended traditional understandings of the administrative state

Smarter Programming of the Female Condom: Increasing Its Impact on HIV Prevention in the Developing World

The purpose of this study was to investigate the relative value of the female condom for HIV prevention within heterosexual relationships in the developing world. In the last ten years, the world has witnessed both historic financial commitments to HIV/AIDS and new prevention options, including biomedical prevention research, male circumcision, and a dramatic scale-up of voluntary counseling and testing. At the same time, where HIV remains at epidemic levels in many countries, there has been a growing commitment to treatment access alongside prevention programs. However, portions of populations, particularly youth and women, remain highly vulnerable to HIV infection. Accordingly, the global health community can benefit from a better understanding of how existing prevention options should be effectively and efficiently delivered to reduce HIV in the developing world. This report provides guidance for the global health community for considering how the female condom fits within the set of prevention interventions currently available

ELVIS: Exploring the Local Volume in Simulations

We introduce a set of high-resolution dissipationless simulations that model the Local Group (LG) in a cosmological context: Exploring the Local Volume in Simulations (ELVIS). The suite contains 48 Galaxy-size halos, each within high-resolution volumes that span 2-5 Mpc in size, and each resolving thousands of systems with masses below the atomic cooling limit. Half of the ELVIS galaxy halos are in paired configurations similar to the Milky Way (MW) and M31; the other half are isolated, mass-matched analogs. We find no difference in the abundance or kinematics of substructure within the virial radii of isolated versus paired hosts. On Mpc scales, however, LG-like pairs average almost twice as many companions and the velocity field is kinematically hotter and more complex. We present a refined abundance matching relation between stellar mass and halo mass that reproduces the observed satellite stellar mass functions of the MW and M31 down to the regime where incompleteness is an issue, $M_\star \sim 5\times 10^5 \, M_\odot$. Within a larger region spanning approximately 3 Mpc, the same relation predicts that there should be $\sim$ 1000 galaxies with $M_\star > 10^{3}\,M_\odot$ awaiting discovery. We show that up to 50% of halos within 1 Mpc of the MW or M31 could be systems that have previously been within the virial radius of either giant. By associating never-accreted halos with gas-rich dwarfs, we show that there are plausibly 50 undiscovered dwarf galaxies with HI masses $> 10^5\,M_\odot$ within the Local Volume. The radial velocity distribution of these predicted gas-rich dwarfs can be used to inform follow-up searches based on ultra-compact high-velocity clouds found in the ALFALFA survey.Comment: 22 pages, 19 figures, 3 tables; v2 -- accepted to MNRAS. Movies, images, and data are available at http://localgroup.ps.uci.edu/elvi