Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

On the Geometry and Mass of Static, Asymptotically AdS Spacetimes, and the Uniqueness of the AdS Soliton

We prove two theorems, announced in hep-th/0108170, for static spacetimes that solve Einstein's equation with negative cosmological constant. The first is a general structure theorem for spacetimes obeying a certain convexity condition near infinity, analogous to the structure theorems of Cheeger and Gromoll for manifolds of non-negative Ricci curvature. For spacetimes with Ricci-flat conformal boundary, the convexity condition is associated with negative mass. The second theorem is a uniqueness theorem for the negative mass AdS soliton spacetime. This result lends support to the new positive mass conjecture due to Horowitz and Myers which states that the unique lowest mass solution which asymptotes to the AdS soliton is the soliton itself. This conjecture was motivated by a nonsupersymmetric version of the AdS/CFT correspondence. Our results add to the growing body of rigorous mathematical results inspired by the AdS/CFT correspondence conjecture. Our techniques exploit a special geometric feature which the universal cover of the soliton spacetime shares with familiar ``ground state'' spacetimes such as Minkowski spacetime, namely, the presence of a null line, or complete achronal null geodesic, and the totally geodesic null hypersurface that it determines. En route, we provide an analysis of the boundary data at conformal infinity for the Lorentzian signature static Einstein equations, in the spirit of the Fefferman-Graham analysis for the Riemannian signature case. This leads us to generalize to arbitrary dimension a mass definition for static asymptotically AdS spacetimes given by Chru\'sciel and Simon. We prove equivalence of this mass definition with those of Ashtekar-Magnon and Hawking-Horowitz.Comment: Accepted version, Commun Math Phys; Added Remark IV.3 and supporting material dealing with non-uniqueness arising from choice of special cycle on the boundary at infinity; 2 new citations added; LaTeX 27 page

Decoherence, Re-coherence, and the Black Hole Information Paradox

We analyze a system consisting of an oscillator coupled to a field. With the field traced out as an environment, the oscillator loses coherence on a very short {\it decoherence timescale}; but, on a much longer {\it relaxation timescale}, predictably evolves into a unique, pure (ground) state. This example of {\it re-coherence} has interesting implications both for the interpretation of quantum theory and for the loss of information during black hole evaporation. We examine these implications by investigating the intermediate and final states of the quantum field, treated as an open system coupled to an unobserved oscillator.Comment: 23 pages, 2 figures included, figures 3.1 - 3.3 available at http://qso.lanl.gov/papers/Papers.htm

Nanostructure of CaO-(Na2O)-Al2O3-SiO2-H2O gels revealed by multinuclear solid-state magic angle spinning and multiple quantum magic angle spinning nuclear magnetic resonance spectroscopy

(Calcium,alkali)-aluminosilicate gel frameworks are the basis of modern cements and alkali-activated materials for sustainable infrastructure and radioactive waste immobilization and also find application in glass alteration, mineral weathering, and zeolite synthesis. Here, we resolve the nanostructure of these gels that dictates mass transport, solubility, and mechanical properties. The key structural motifs comprising hydrous (calcium,alkali)-aluminosilicate gels are identified via 17O, 23Na, and 27Al triple-quantum magic angle spinning and 29Si magic angle spinning nuclear magnetic resonance spectroscopy of a novel class of stoichiometrically controlled 17O-enriched multiphase gels. Increased Ca content promotes low-Al, high-Ca chain-structured “C-S-H-type” products exhibiting significant nanostructural ordering, low levels of chain cross-linking, predominant Ca coordination of nonbridging oxygen atoms, and an increase in proton association with CaO layers to form Ca–OH sites. Al substitution is identified in multiple sites in the silicate chains, including cross-linking, bridging, and pairing tetrahedra. Increased Al content increases the proportion of cross-linking sites and gel disorder. The large increase in SiIV–O–AlIV sites increases the relative amounts of Na+ and AlV species charge-balancing AlO4– tetrahedra and results in the formation of an additional disordered low-calcium, framework-structured alkali aluminosilicate (“N-A-S-H-type”) gel, with high Al and Na contents. Changes in bulk composition significantly alter the nanostructures of the C-S-H-type and N-A-S-H-type gels. Mean SiIV–O–AlIV bond angles for each type of AlIV site environment are highly consistent, with compositional changes dictating the relative proportions of individual AlIV species but not altering the local structure of each AlIV site. These findings reveal the molecular interactions governing the (calcium,alkali)-aluminosilicate gel nanostructure, which are crucial in controlling material properties and durability

Measurement invariance of the short Warwick-Edinburgh mental wellbeing scale and latent mean differences (SWEMWBS) in young people by current care status

Purpose Studying mental wellbeing requires the use of reliable, valid, and practical assessment tools, such as the Short version of the Warwick-Edinburgh Mental Wellbeing Scale (SWEMWBS). Research on the mental wellbeing of children in care is sparse. The current study aims to: (1) examine the unidimensionality of SWEMWBS; (2) assess measurement invariance of SWEMWBS across children and young people in care compared to their peers not in care; and (3) investigate the latent factor mean differences between care status groups. Methods We used data from the 2017 School Health Research Network Student Health and Wellbeing (SHW) survey, completed by 103,971 students in years 7 to 11 from 193 secondary schools in Wales. The final data include a total of 2,795 participants (46% boys), which includes all children in care and a sub-sample of children not in care who completed the SWEMWBS scale fully and answered questions about their living situation. Results Confirmatory factor analysis supported the unidimensionality of SWEMWBS. The SWEMWBS is invariant across groups of young people in foster, residential and kinship care compared to children and young people not in care at configural, metric and scalar levels. Findings from latent mean comparisons showed that young people in care reported lower mental wellbeing than their peers, with those in residential care reporting the lowest scores. Conclusions Findings suggest that SWEMWBS is a valid scale for measuring differences in mental wellbeing for young people in care similar to the population

Using latent class analysis to explore complex associations between socioeconomic status and adolescent health and wellbeing

Purpose Research demonstrates a strong socioeconomic gradient in health and well-being. However, many studies rely on unidimensional measures of socioeconomic status (SES) (e.g. educational qualifications, household income), and there is often a more limited consideration of how facets of SES combine to impact well-being. This paper develops a multidimensional measure of SES, drawing on family and school-level factors, to provide more nuanced understandings of socioeconomic patterns in adolescent substance use and mental well-being. Methods Data from the Student Health and Wellbeing Survey from Wales, UK was employed. The sample compromised 22,372 students and we used latent class analysis to identify distinct groups using three measures of SES. These classes were then used to estimate mental well-being, internalizing symptoms, and substance use. Results The five-class solution offered the best fit. Findings indicated distinct classes of families as follows: “nonworking,” “deprived working families,” “affluent families in deprived schools,” “lower affluence,” and “higher affluence.” There was a clear relationship among the classes and mental well-being, internalizing symptoms, smoking, and cannabis use; alcohol was the exception to this. Conclusions The identification of these classes led to a fuller understanding of the health and well-being effects of SES, showing clearer patterning in health behaviors that often is not captured in research. The implications for adolescent health and well-being are discussed, including considerations for future research

Risk behaviours associated with dating and relationship violence among 11–16 year olds in Wales: results from the 2019 student health and wellbeing survey

(1) Background: This study examines the associations between risk behaviours and adolescent emotional and physical dating and relationship violence (DRV) victimisation and perpetration, and how these vary by gender. The risk behaviours explored include bullying, cyberbullying, sexting, alcohol, and cannabis use; (2) Methods: Cross-sectional self-report data from the School Health Research Network (SHRN) 2019 Student Health Wellbeing (SHW) survey of 48,397 students aged 11–16 from 149 schools across Wales were analysed using single and multiple-behaviour logistic regression models to explore the associations between each risk behaviour and emotional and physical DRV victimisation and perpetration; (3) Results: Bivariate analyses revealed a statistically significant association between DRV and all risk behaviours. In multivariate analyses, students who reported bullying, cyberbullying, sexting, and substance use, compared to those that had not, had significantly higher odds of experiencing and perpetrating emotional and physical DRV; and (4) Conclusions: Future studies on DRV should consider a mixed-methods approach to explore the context in which DRV and risk behaviours interrelate. Results from this study indicate the possibility that prevention and intervention programmes in school settings that seek to develop healthy school environments and peer-to-peer relationships, could inadvertently reduce the occurrence of future DRV and associated risk behaviours

The Seyfert-LINER Galaxy NGC 7213: An XMM-Newton Observation

We examine the XMM X-ray spectrum of the LINER-AGN NGC 7213, which is best fit with a power law, K-alpha emission lines from Fe I, Fe XXV and Fe XXVI and a soft X-ray collisionally ionised thermal plasma with kT=0.18 +0.03/-0.01 keV. We find a luminosity of 7x10^(-4) L_Edd, and a lack of soft X-ray excess emission, suggesting a truncated accretion disc. NGC 7213 has intermediate X-ray spectral properties, between those of the weak AGN found in the LINER M81 and higher luminosity Seyfert galaxies. This supports the notion of a continuous sequence of X-ray properties from the Galactic Centre through LINER galaxies to Seyferts, likely determined by the amount of material available for accretion in the central regions.Comment: 7 pages, 2 figures. To appear in From X-ray Binaries to Quasars: Black Hole Accretion on All Mass Scales, ed. T. J. Maccarone, R. P. Fender, and L. C. Ho (Dordrecht: Kluwer

Swift observations of the X-ray and UV evolution of V2491 Cyg (Nova Cyg 2008 No. 2)

We present extensive, high-density Swift observations of V2491 Cyg (Nova Cyg 2008 No. 2). Observing the X-ray emission from only one day after the nova discovery, the source is followed through the initial brightening, the Super-Soft Source phase and back to the pre-outburst flux level. The evolution of the spectrum throughout the outburst is demonstrated. The UV and X-ray light-curves follow very different paths, although changes occur in them around the same times, indicating a link between the bands. Flickering in the late-time X-ray data indicates the resumption of accretion. We show that if the white dwarf is magnetic, it would be among the most magnetic known; the lack of a periodic signal in our later data argues against a magnetic white dwarf, however. We also discuss the possibility that V2491 Cyg is a recurrent nova, providing recurrence timescale estimates.Comment: 12 pages, 8 figure (2 in colour), accepted for publication in MNRA

Averaged Energy Conditions and Evaporating Black Holes

In this paper the averaged weak (AWEC) and averaged null (ANEC) energy conditions, together with uncertainty principle-type restrictions on negative energy (``quantum inequalities''), are examined in the context of evaporating black hole backgrounds in both two and four dimensions. In particular, integrals over only half-geodesics are studied. We determine the regions of the spacetime in which the averaged energy conditions are violated. In all cases where these conditions fail, there appear to be quantum inequalities which bound the magnitude and extent of the negative energy, and hence the degree of the violation. The possible relevance of these results for the validity of singularity theorems in evaporating black hole spacetimes is discussed.Comment: Sections 2.1 and 2.2 have been revised and some erroneous statements corrected. The main conclusions and the figures are unchanged. 27 pp, plain Latex, 3 figures available upon reques