Minimizing the average distance to a closest leaf in a phylogenetic tree

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally-derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this paper we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, while PAM only gives a solution for the pre-specified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, while the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.Comment: Please contact us with any comments or questions

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Signatures of Gate-Tunable Superconductivity in Trilayer Graphene/Boron Nitride Moir\'e Superlattice

Understanding the mechanism of high temperature (high Tc) superconductivity is a central problem in condensed matter physics. It is often speculated that high Tc superconductivity arises from a doped Mott insulator as described by the Hubbard model. An exact solution of the Hubbard model, however, is extremely challenging due to the strong electron-electron correlation. Therefore, it is highly desirable to experimentally study a model Hubbard system in which the unconventional superconductivity can be continuously tuned by varying the Hubbard parameters. Here we report signatures of tunable superconductivity in ABC-trilayer graphene (TLG) / boron nitride (hBN) moir\'e superlattice. Unlike "magic angle" twisted bilayer graphene, theoretical calculations show that under a vertical displacement field the ABC-TLG/hBN heterostructure features an isolated flat valence miniband associated with a Hubbard model on a triangular superlattice. Upon applying such a displacement field we find experimentally that the ABC-TLG/hBN superlattice displays Mott insulating states below 20 Kelvin at 1/4 and 1/2 fillings, corresponding to 1 and 2 holes per unit cell, respectively. Upon further cooling, signatures of superconducting domes emerge below 1 kelvin for the electron- and hole-doped sides of the 1/4 filling Mott state. The electronic behavior in the TLG/hBN superlattice is expected to depend sensitively on the interplay between the electron-electron interaction and the miniband bandwidth, which can be tuned continuously with the displacement field D. By simply varying the D field, we demonstrate transitions from the candidate superconductor to Mott insulator and metallic phases. Our study shows that TLG/hBN heterostructures offer an attractive model system to explore rich correlated behavior emerging in the tunable triangular Hubbard model.Comment: 14 pages, 4 figure

Hierarchical Star Formation in Nearby LEGUS Galaxies

Hierarchical structure in ultraviolet images of 12 late-type LEGUS galaxies is studied by determining the numbers and fluxes of nested regions as a function of size from ~1 to ~200 pc, and the number as a function of flux. Two starburst dwarfs, NGC 1705 and NGC 5253, have steeper number-size and flux-size distributions than the others, indicating high fractions of the projected areas filled with star formation. Nine subregions in 7 galaxies have similarly steep number-size slopes, even when the whole galaxies have shallower slopes. The results suggest that hierarchically structured star-forming regions several hundred parsecs or larger represent common unit structures. Small galaxies dominated by only a few of these units tend to be starbursts. The self-similarity of young stellar structures down to parsec scales suggests that star clusters form in the densest parts of a turbulent medium that also forms loose stellar groupings on larger scales. The presence of super star clusters in two of our starburst dwarfs would follow from the observed structure if cloud and stellar subregions more readily coalesce when self-gravity in the unit cell contributes more to the total gravitational potential.Comment: 9 pages, 4 figures, accepted for ApJ

Evaluating Systematic Dependencies of Type Ia Supernovae: The Influence of Deflagration to Detonation Density

We explore the effects of the deflagration to detonation transition (DDT) density on the production of Ni-56 in thermonuclear supernova explosions (type Ia supernovae). Within the DDT paradigm, the transition density sets the amount of expansion during the deflagration phase of the explosion and therefore the amount of nuclear statistical equilibrium (NSE) material produced. We employ a theoretical framework for a well-controlled statistical study of two-dimensional simulations of thermonuclear supernovae with randomized initial conditions that can, with a particular choice of transition density, produce a similar average and range of Ni-56 masses to those inferred from observations. Within this framework, we utilize a more realistic "simmered" white dwarf progenitor model with a flame model and energetics scheme to calculate the amount of Ni-56 and NSE material synthesized for a suite of simulated explosions in which the transition density is varied in the range 1-3x10^7 g/cc. We find a quadratic dependence of the NSE yield on the log of the transition density, which is determined by the competition between plume rise and stellar expansion. By considering the effect of metallicity on the transition density, we find the NSE yield decreases by 0.055 +/- 0.004 solar masses for a 1 solar metallicity increase evaluated about solar metallicity. For the same change in metallicity, this result translates to a 0.067 +/- 0.004 solar mass decrease in the Ni-56 yield, slightly stronger than that due to the variation in electron fraction from the initial composition. Observations testing the dependence of the yield on metallicity remain somewhat ambiguous, but the dependence we find is comparable to that inferred from some studies.Comment: 15 pages, 13 figures, accepted to ApJ on July 6, 201

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

Beliefs about the Minds of Others Influence How We Process Sensory Information

Attending where others gaze is one of the most fundamental mechanisms of social cognition. The present study is the first to examine the impact of the attribution of mind to others on gaze-guided attentional orienting and its ERP correlates. Using a paradigm in which attention was guided to a location by the gaze of a centrally presented face, we manipulated participants' beliefs about the gazer: gaze behavior was believed to result either from operations of a mind or from a machine. In Experiment 1, beliefs were manipulated by cue identity (human or robot), while in Experiment 2, cue identity (robot) remained identical across conditions and beliefs were manipulated solely via instruction, which was irrelevant to the task. ERP results and behavior showed that participants' attention was guided by gaze only when gaze was believed to be controlled by a human. Specifically, the P1 was more enhanced for validly, relative to invalidly, cued targets only when participants believed the gaze behavior was the result of a mind, rather than of a machine. This shows that sensory gain control can be influenced by higher-order (task-irrelevant) beliefs about the observed scene. We propose a new interdisciplinary model of social attention, which integrates ideas from cognitive and social neuroscience, as well as philosophy in order to provide a framework for understanding a crucial aspect of how humans' beliefs about the observed scene influence sensory processing

Emission and Absorption Properties of Low-Mass Type 2 Active Galaxies with XMM-Newton

We present XMM-Newton observations of four low-redshift Seyfert galaxies selected to have low host luminosities (M_g>-20 mag) and small stellar velocity dispersions (sigma_star<45 km/s), which are among the smallest stellar velocity dispersions found in any active galaxies. These galaxies show weak or no broad optical emission lines and have likely black hole masses <10^6 M_sun. Three out of four objects were detected with >3sigma significance in ~25 ks exposures and two observations had high enough signal-to-noise ratios for rudimentary spectral analysis. We calculate hardness ratios (-0.43 to 0.01) for the three detected objects and use them to estimate photon indices in the range of Gamma=1.1-1.8. Relative to [OIII], the type 2 objects are X-ray faint in comparison with Seyfert 1 galaxies, suggesting that the central engines are obscured. We estimate the intrinsic absorption of each object under the assumption that the [OIII] emission line luminosities are correlated with the unabsorbed X-ray luminosity. The results are consistent with moderate (N_H~10^22 cm^-2) absorption over the Galactic values in three of the four objects, which might explain the non-detection of broad-line emission in optical spectra. One object in our sample, SDSS J110912.40+612346.7, is a near identical type 2 counterpart of the late-type Seyfert 1 galaxy NGC 4395. While the two objects have very similar [OIII] luminosities, the type 2 object has an X-ray/[OIII] flux ratio nearly an order of magnitude lower than NGC 4395. The most plausible explanation for this difference is absorption of the primary X-ray continuum of the type 2 object, providing an indication that obscuration-based unified models of active galaxies can apply even at the lowest luminosities seen among Seyfert nuclei, down to L_bol~10^40-10^41 erg/s.Comment: 5 figures, 3 tables, accepted for publication in Ap

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges