The generalized Robinson-Foulds metric

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Effect of material, geometry, surface treatment and environment on the shear strength of single lap joints

The single lap joint is the most studied type of adhesive joint in the literature. However, the joint strength prediction of such joints is still a controversial issue as it involves a lot of factors that are difficult to quantify such as the overlap length, the yielding of the adherend, the plasticity of the adhesive and the bondline thickness. The most complicated case is that where the adhesive is brittle and the overlap long. In any case, there is still a problem that is even more difficult to take into account which is the durability. There is a lack of experimental data and design criteria when the joint is subjected to high, low or variable temperature and/or humidity. The objective of this work is to carry out and quantify the various variables affecting the strength of single lap joints in long term, especially the effect of the surface preparation. The Taguchi method is used to decrease the number of experimental tests. The effect of material, geometry, surface treatment and environment is studied and it is shown that the main effect is that of the overlap length. In order to quantify the influence of the adhesive (toughness and thickness), the adherend (yield strength and thickness), the overlap, the test speed, the surface preparation and durability on the lap shear strength, the experimental design technique of Taguchi was used in the present study. An experimental matrix of eighteen tests was designed and each test was repeated three times. The influence of the eight previously-mentioned variables could be assessed using the statistical software Statview®. In this paper a simple predictive equation is proposed for the design of single lap joints

Alcohol Marketing during the UEFA EURO 2016 Football Tournament: A Frequency Analysis

This study examined the frequency and nature of alcohol marketing references in broadcasts of the 2016 UEFA (Union of European Football Associations) European Championships football tournament in the United Kingdom (UK). Eighteen matches from across the tournament were recorded in full as broadcast in the UK, including all four matches featuring the English national team and all seven featuring the French national team. All visual and verbal references to alcohol marketing were recorded using a tool with high inter-rater reliability. A total of 2213 alcohol marketing references were recorded, an average of 122.94 per broadcast and 0.65 per broadcast minute (0.52 per minute in-play and 0.80 per minute out-of-play). Almost all references were visual (97.5%), with 77.9% occurring around the pitch border. Almost all (90.6%) were indirect references to alcohol brands (e.g., references to well-known slogans), compared to only 9.4% direct references to brands (e.g., brand names). The frequency of references to alcohol marketing was high. Although the overall proportion of direct brand references was low, the high proportion of indirect references demonstrates that alcohol producers were able to circumvent the French national law governing alcohol marketing (the Loi Évin) using indirect “alibi marketing”. To ensure the spirit of the Loi Évin regulations are achieved, stricter enforcement may be required to limit exposure to alcohol marketing, particularly for young peopleThis research was funded by the Institute of Alcohol Studies, Scottish Health Actions on Alcohol Problems and Alcohol Action Ireland

Tracking Multiple Topics for Finding Interesting Articles

We introduce multiple topic tracking (MTT) for iScore to better recommend news articles for users with multiple interests and to address changes in user interests over time. As an extension of the basic Rocchio algorithm, traditional topic detection and tracking, and single-pass clustering, MTT maintains multiple interest profiles to identify interesting articles for a specific user given user-feedback. Focusing on only interesting topics enables iScore to discard useless profiles to address changes in user interests and to achieve a balance between resource consumption and classification accuracy. iScore is able to achieve higher quality results than traditional methods such as the Rocchio algorithm. We identify several operating parameters that work well for MTT. Using the same parameters, we show that MTT alone yields high quality results for recommending interesting articles from several corpora. The inclusion of MTT improves iScore's performance by 25% in recommending news articles from the Yahoo! News RSS feeds and the TREC11 adaptive filter article collection. And through a small user study, we show that iScore can still perform well when only provided with little user feedback

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

Belle II Technical Design Report

The Belle detector at the KEKB electron-positron collider has collected almost 1 billion Y(4S) events in its decade of operation. Super-KEKB, an upgrade of KEKB is under construction, to increase the luminosity by two orders of magnitude during a three-year shutdown, with an ultimate goal of 8E35 /cm^2 /s luminosity. To exploit the increased luminosity, an upgrade of the Belle detector has been proposed. A new international collaboration Belle-II, is being formed. The Technical Design Report presents physics motivation, basic methods of the accelerator upgrade, as well as key improvements of the detector.Comment: Edited by: Z. Dole\v{z}al and S. Un

Dysconnection in schizophrenia: from abnormal synaptic plasticity to failures of self-monitoring

Over the last 2 decades, a large number of neurophysiological and neuroimaging studies of patients with schizophrenia have furnished in vivo evidence for dysconnectivity, ie, abnormal functional integration of brain processes. While the evidence for dysconnectivity in schizophrenia is strong, its etiology, pathophysiological mechanisms, and significance for clinical symptoms are unclear. First, dysconnectivity could result from aberrant wiring of connections during development, from aberrant synaptic plasticity, or from both. Second, it is not clear how schizophrenic symptoms can be understood mechanistically as a consequence of dysconnectivity. Third, if dysconnectivity is the primary pathophysiology, and not just an epiphenomenon, then it should provide a mechanistic explanation for known empirical facts about schizophrenia. This article addresses these 3 issues in the framework of the dysconnection hypothesis. This theory postulates that the core pathology in schizophrenia resides in aberrant N-methyl-D-aspartate receptor (NMDAR)–mediated synaptic plasticity due to abnormal regulation of NMDARs by neuromodulatory transmitters like dopamine, serotonin, or acetylcholine. We argue that this neurobiological mechanism can explain failures of self-monitoring, leading to a mechanistic explanation for first-rank symptoms as pathognomonic features of schizophrenia, and may provide a basis for future diagnostic classifications with physiologically defined patient subgroups. Finally, we test the explanatory power of our theory against a list of empirical facts about schizophrenia

Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ

The recently characterised 299-residue human XLF/Cernunnos protein plays a crucial role in DNA repair by non-homologous end joining (NHEJ) and interacts with the XRCC4–DNA Ligase IV complex. Here, we report the crystal structure of the XLF (1–233) homodimer at 2.3 Å resolution, confirming the predicted structural similarity to XRCC4. The XLF coiled-coil, however, is shorter than that of XRCC4 and undergoes an unexpected reverse in direction giving rise to a short distorted four helical bundle and a C-terminal helical structure wedged between the coiled-coil and head domain. The existence of a dimer as the major species is confirmed by size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering and other biophysical methods. We show that the XLF structure is not easily compatible with a proposed XRCC4:XLF heterodimer. However, we demonstrate interactions between dimers of XLF and XRCC4 by surface plasmon resonance and analyse these in terms of surface properties, amino-acid conservation and mutations in immunodeficient patients. Our data are most consistent with head-to-head interactions in a 2:2:1 XRCC4:XLF:Ligase IV complex

High prevalence of high risk human papillomavirus-capsid antibodies in human immunodeficiency virus-seropositive men: a serological study

BACKGROUND: Serological study of human papillomavirus (HPV)-antibodies in order to estimate the HPV-prevalence as risk factor for the development of HPV-associated malignancies in human immunodeficiency virus (HIV)-positive men. METHODS: Sera from 168 HIV-positive men and 330 HIV-negative individuals (including 198 controls) were tested using a direct HPV-ELISA specific to HPV-6, -11, -16, -18, -31 and bovine PV-1 L1-virus-like particles. Serological results were correlated with the presence of HPV-associated lesions, the history of other sexually transmitted diseases (STD) and HIV classification groups. RESULTS: In HIV-negative men low risk HPV-antibodies were prevailing and associated with condylomatous warts (25.4%). Strikingly, HIV-positive men were more likely to have antibodies to the high-risk HPV types -16, -18, -31, and low risk antibodies were not increased in a comparable range. Even those HIV-positive heterosexual individuals without any HPV-associated lesions exhibited preferentially antibody responses to the oncogenic HPV-types (cumulative 31.1%). The highest antibody detection rate (88,8%) was observed within the subgroup of nine HIV-positive homosexual men with anogenital warts. Three HIV-positive patients had HPV-associated carcinomas, in all of them HPV-16 antibodies were detected. Drug use and mean CD4-cell counts on the day of serologic testing had no influence on HPV-IgG antibody prevalence, as had prior antiretroviral therapy or clinical category of HIV-disease. CONCLUSION: High risk HPV-antibodies in HIV-infected and homosexual men suggest a continuous exposure to HPV-proteins throughout the course of their HIV infection, reflecting the known increased risk for anogenital malignancies in these populations. The extensive increase of high risk antibodies (compared to low risk antibodies) in HIV-positive patients cannot be explained by differences in exposure history alone, but suggests defects of the immunological control of oncogenic HPV-types. HPV-serology is economic and can detect past or present HPV-infection, independently of an anatomical region. Therefore HPV-serology could help to better understand the natural history of anogenital HPV-infection in HIV-positive men in the era of antiretroviral therapy