New features in the simulation of neutrino oscillation experiments with GLoBES 3.0

We present Version 3.0 of the GLoBES (``General Long Baseline Experiment Simulator'') software, which is a simulation tool for short- and long-baseline neutrino oscillation experiments. As a new feature, GLoBES 3.0 allows for user-defined systematical errors, which can also be used to simulate experiments with multiple discrete sources and detectors. In addition, the combination with external information, such as from different experiment classes, is simplified. As far as the probability calculation is concerned, GLoBES now provides an interface for the inclusion of non-standard physics without re-compilation of the software. The set of experiment prototypes coming with GLoBES has been updated. For example, built-in fluxes are now provided for the simulation of beta beams.Comment: 14 pages, 3 figures, 1 table. Definition of chi2 refined, version to appear in Comput. Phys. Commun. GLoBES software available at http://www.mpi-hd.mpg.de/lin/globes

Perspectives on Tobacco Product Waste: A Survey of Framework Convention Alliance Members' Knowledge, Attitudes, and Beliefs.

Cigarette butts (tobacco product waste (TPW)) are the single most collected item in environmental trash cleanups worldwide. This brief descriptive study used an online survey tool (Survey Monkey) to assess knowledge, attitudes, and beliefs among individuals representing the Framework Convention Alliance (FCA) about this issue. The FCA has about 350 members, including mainly non-governmental tobacco control advocacy groups that support implementation of the World Health Organization's (WHO) Framework Convention on Tobacco Control (FCTC). Although the response rate (28%) was low, respondents represented countries from all six WHO regions. The majority (62%) have heard the term TPW, and nearly all (99%) considered TPW as an environmental harm. Most (77%) indicated that the tobacco industry should be responsible for TPW mitigation, and 72% felt that smokers should also be held responsible. This baseline information may inform future international discussions by the FCTC Conference of the Parties (COP) regarding environmental policies that may be addressed within FCTC obligations. Additional research is planned regarding the entire lifecycle of tobacco's impact on the environment

Bounds for phylogenetic network space metrics

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set X of taxa. This space, denoted N(X)N(X) , is defined in terms of two operations on networks—the nearest neighbor interchange and triangle operations—which can be used to transform any network with leaf set X into any other network with that leaf set. In particular, it gives rise to a metric d on N(X)N(X) which is given by the smallest number of operations required to transform one network in N(X)N(X) into another in N(X)N(X) . The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric d as well as a related metric dNNIdNNI which arises when restricting d to the subset of N(X)N(X) consisting of all networks with 2(|X|−1+i)2(|X|−1+i) vertices, i≥1i≥1 . We also introduce two new metrics on networks—the SPR and TBR metrics—which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms

The new organic import scheme in the EU

The Powerpoint presentations were presented at the session 'The new organic import scheme in the EU' at the BioFach Congress 200

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-

The Southern 2MASS AGN Survey: spectroscopic follow-up with 6dF

The Two Micron All-Sky Survey (2MASS) has provided a uniform photometric catalog to search for previously unknown red AGN and QSOs. We have extended the search to the southern equatorial sky by obtaining spectra for 1182 AGN candidates using the 6dF multifibre spectrograph on the UK Schmidt Telescope. These were scheduled as auxiliary targets for the 6dF Galaxy Redshift Survey. The candidates were selected using a single color cut of J - Ks > 2 to Ks ~ 15.5 and a galactic latitude of |b|>30 deg. 432 spectra were of sufficient quality to enable a reliable classification. 116 sources (or ~27%) were securely classified as type 1 AGN, 20 as probable type 1s, and 57 as probable type 2 AGN. Most of them span the redshift range 0.05<z<0.5 and only 8 (or ~6%) were previously identified as AGN or QSOs. Our selection leads to a significantly higher AGN identification rate amongst local galaxies (>20%) than in any previous galaxy survey. A small fraction of the type 1 AGN could have their optical colors reddened by optically thin dust with A_V<2 mag relative to optically selected QSOs. A handful show evidence for excess far-IR emission. The equivalent width (EW) and color distributions of the type 1 and 2 AGN are consistent with AGN unified models. In particular, the EW of the [OIII] emission line weakly correlates with optical--near-IR color in each class of AGN, suggesting anisotropic obscuration of the AGN continuum. Overall, the optical properties of the 2MASS red AGN are not dramatically different from those of optically-selected QSOs. Our near-IR selection appears to detect the most near-IR luminous QSOs in the local universe to z~0.6 and provides incentive to extend the search to deeper near-IR surveys.Comment: 57 pages, 12 figures, 4 tables, to appear in vol.27/4 of Publications of the Astronomical Society of Australia (PASA

Reliable Eigenspectra for New Generation Surveys

We present a novel technique to overcome the limitations of the applicability of Principal Component Analysis to typical real-life data sets, especially astronomical spectra. Our new approach addresses the issues of outliers, missing information, large number of dimensions and the vast amount of data by combining elements of robust statistics and recursive algorithms that provide improved eigensystem estimates step-by-step. We develop a generic mechanism for deriving reliable eigenspectra without manual data censoring, while utilising all the information contained in the observations. We demonstrate the power of the methodology on the attractive collection of the VIMOS VLT Deep Survey spectra that manifest most of the challenges today, and highlight the improvements over previous workarounds, as well as the scalability of our approach to collections with sizes of the Sloan Digital Sky Survey and beyond.Comment: 7 pages, 3 figures, accepted to MNRA

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks