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

‘Draw, write and tell’. A literature review and methodological development on the ‘draw and write’ research method.

The creative research method ‘draw and write’ has been used in health, social care and education research for several decades. A literature search of studies utilising this method was conducted during the planning stages of a study exploring primary school children’s perceptions of infant feeding. A review of this literature noted a range of benefits of ‘draw and write’ in enabling child participation. However, it also identified that the method has been used inconsistently and found that there are issues for researchers in relation to interpretation of creative work and analysis of data. As a result of this, an improvement on this method, entitled ‘draw, write and tell’, was developed in an attempt to provide a more child-orientated and consistent approach to data collection, interpretation and analysis. This article identifies the issues relating to ‘draw and write’ and describes the development and application of ‘draw, write and tell’ as a case study, noting its limitations and benefit

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase

Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown

Algebraic Comparison of Partial Lists in Bioinformatics

The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or just within a meta-analysis comparison, instead of one list it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained. Here we introduce a method, based on the algebraic theory of symmetric groups, for studying the variability between lists ("list stability") in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated first on synthetic data in a gene filtering task and then for finding gene profiles on a recent prostate cancer dataset

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

Surface cleaning technologies for the removal of crosslinked epoxide resin

This study provides details of the use of laser ablation and sodium hydride cleaning processes for the removal of crosslinked epoxide and other residues from resin transfer moulding (RTM) tool substrates, as used in the aerospace industry. The requirement for removal of such contamination is so that the mould can be re-used, following the subsequent application of an external release agent. These tools are, typically, fabricated from steel, nickel or CFRP composite materials; this paper focuses on the use of nickel substrates. The requirement to clean large surface areas quickly to satisfy commercial restraints, compromises the degree of absolute cleanliness that can be obtained. However, in applications where cleaning time is not a constraint, laser cleaning can be a very gentle and efficient process; typically Nd:YAG lasers find application in this area. In contrast, high power lasers are desirable for industrial scale applications where large areas need to be cleaned quickly. In this instance pulsed CO2 lasers can be used. The use of sodium hydride was also found to be highly successful in removing crosslinked organic contamination providing that suitable hard rinse and drying operations were also carried out

Using the NILOA Transparency Framework: It\u27s All About the Process

When the St. John Fisher College Educational Assessment Leadership Team set out to make assessment information readily accessible, they looked to the NILOA Transparency Framework to serve as a guiding template. Recognizing its use nationally to clearly communicate the six assessment components with hexagons, they saw the NILOA model as the ideal format for the design of the institutional assessment website. Assessment results could be organized with the comprehensive, straightforward NILOA graphic. What they did not expect, however, was that the process of adopting the framework would transform not just how assessment “looked”, but how they saw it as well

Tobacco, e-cigarette and alcohol content in popular UK soap operas: a content analysis to explore changes in social norms and scene location over time

Background Exposure to tobacco and alcohol on-screen promotes use and despite regulations and policies to limit impact, these behaviours remain common. We report a longitudinal analysis of tobacco, e-cigarette and alcohol content in three popular UK television soap operas, to examine changing social norms between 2002-2022. Methods We used one-minute interval coding to measure content in programmes in two one-week periods in three years (2002, 2012 and 2022). Change in probability of actual and implied use of tobacco, e-cigarette and alcohol over time was examined using logistic regression. Results We coded 2505 intervals from 78 episodes. Tobacco content occurred in 22% of episodes and significantly decreased from 2002 to 2022 (OR 0.15 95% CI 0.06-0.40). Tobacco use changed over time with decreasing use indoors and increasing use outdoors. No e-cigarette use was identified. Alcohol content was found in 88% of episodes and while it also significantly decreased over time (OR 0.78 95% CI 0.61 – 0.99) it featured in 20% of broadcast minutes in 2022. Alcohol use in homes increased over time. Conclusion While tobacco imagery is increasingly rare on television, alcohol content has remained common. Current regulations are not sufficient to reduce exposure. Soap opera producers should consider the impact of on-screen tobacco and alcohol use and opportunities to change social norms and help protect future generations