Tree-Based Unrooted Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms. Correction available at dx.doi.org/10.1007/s11538-018-0530-

Plasma Dynamics

Contains reports on three research projects.U.S. Department of Energy (Contract DE-ACO2-78ET-51013)National Science Foundation (Grant ECS82-13430)U.S. Air Force - Office of Scientific Research (Contract F33615-81-K-1426

Plasma Dynamics

Contains reports on six research projects.National Science Foundation (Grant ECS82-00646)National Science Foundation (Grant ECS82-13485)U.S. Air Force - Office of Scientific Research (Contract F33615-81-K-1426)U.S. Air Force - Office of Scientific Research (Contract F49620-83-C-0008)U.S. Air Force - Office of Scientific Research (Contract AFOSR-84-0026)U.S. Navy - Office of Naval Research (Contract N00014-83-K-2024)Sandia National Laboratory (Contract 31-5606)Sandia National Laboratory (Contract 48-5725)U.S. Department of Energy (Contract DE-ACO2-78ET-51013)National Science Foundation (Grant ECS82-13430

The potential of video imagery from worldwide cabled observatory networks to provide information supporting fish-stock and biodiversity assessment

Seafloor multiparametric fibre-optic-cabled video observatories are emerging tools for standardized monitoring programmes, dedicated to the production of real-time fishery-independent stock assessment data. Here, we propose that a network of cabled cameras can be set up and optimized to ensure representative long-term monitoring of target commercial species and their surrounding habitats. We highlight the importance of adding the spatial dimension to fixed-point-cabled monitoring networks, and the need for close integration with Artificial Intelligence pipelines, that are necessary for fast and reliable biological data processing. We then describe two pilot studies, exemplary of using video imagery and environmental monitoring to derive robust data as a foundation for future ecosystem-based fish-stock and biodiversity management. The first example is from the NE Pacific Ocean where the deep-water sablefish (Anoplopoma fimbria) has been monitored since 2010 by the NEPTUNE cabled observatory operated by Ocean Networks Canada. The second example is from the NE Atlantic Ocean where the Norway lobster (Nephrops norvegicus) is being monitored using the SmartBay observatory developed for the European Multidisciplinary Seafloor and water column Observatories. Drawing from these two examples, we provide insights into the technological challenges and future steps required to develop full-scale fishery-independent stock assessments.This work was funded by the following project activities: ARIM (Autonomous Robotic sea-floor Infrastructure for benthopelagic Monitoring; MartTERA ERA-Net Cofound), ARCHES (Autonomous Robotic Networks to Help Modern Societies; German Helmholtz Association), RESBIO (TEC2017-87861-R; Ministerio de Ciencia, Innovación y Universidades, Spanish Government), RESNEP (CTM2017-82991-C2-1-R; Ministerio de Ciencia, Innovación y Universidades, Spanish Government), and SmartLobster (EMSO-LINK Trans National Access-TNA). The EMSO_SmartBay cabled observatory was funded by Science Foundation Ireland (SFI) as part of a SFI Research Infrastructure Award Grant No. 12/RI/2331.Peer ReviewedPostprint (author's final draft

Measurements of branching fraction ratios and CP-asymmetries in suppressed B^- -> D(-> K^+ pi^-)K^- and B^- -> D(-> K^+ pi^-)pi^- decays

We report the first reconstruction in hadron collisions of the suppressed decays B^- -> D(-> K^+ pi^-)K^- and B^- -> D(-> K^+ pi^-)pi^-, sensitive to the CKM phase gamma, using data from 7 fb^-1 of integrated luminosity collected by the CDF II detector at the Tevatron collider. We reconstruct a signal for the B^- -> D(-> K^+ pi^-)K^- suppressed mode with a significance of 3.2 standard deviations, and measure the ratios of the suppressed to favored branching fractions R(K) = [22.0 \pm 8.6(stat)\pm 2.6(syst)]\times 10^-3, R^+(K) = [42.6\pm 13.7(stat)\pm 2.8(syst)]\times 10^-3, R^-(K)= [3.8\pm 10.3(stat)\pm 2.7(syst]\times 10^-3, as well as the direct CP-violating asymmetry A(K) = -0.82\pm 0.44(stat)\pm 0.09(syst) of this mode. Corresponding quantities for B^- -> D(-> K^+ pi^-)pi^- decay are also reported.Comment: 8 pages, 1 figure, accepted by Phys.Rev.D Rapid Communications for Publicatio

1st International consensus guidelines for advanced breast cancer (ABC 1)

The 1st international Consensus Conference for Advanced Breast Cancer (ABC 1) took place on November 2011, in Lisbon. Consensus guidelines for the management of this disease were developed. This manuscript summarizes these international consensus guidelines

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Plasma Dynamics

Contains reports on four research projects.National Science Foundation (Grant ECS82-13485)University of Maryland (Subcontract A200728)U.S. Air Force - Office of Scientific Research (Grant AFOSR-84-0026B)U.S. Department of Energy (Contract DE-ACO2-78-ET-51013)National Science Foundation (Grant ECS82-13430