Lateral transfer in Stochastic Dollo models

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages and obtain an improved fit over the corresponding model without lateral transfer.Comment: Improvements suggested by reviewer

Machine learning -- based diffractive imaging with subwavelength resolution

Far-field characterization of small objects is severely constrained by the diffraction limit. Existing tools achieving sub-diffraction resolution often utilize point-by-point image reconstruction via scanning or labelling. Here, we present a new imaging technique capable of fast and accurate characterization of two-dimensional structures with at least wavelength/25 resolution, based on a single far-field intensity measurement. Experimentally, we realized this technique resolving the smallest-available to us 180-nm-scale features with 532-nm laser light. A comprehensive analysis of machine learning algorithms was performed to gain insight into the learning process and to understand the flow of subwavelength information through the system. Image parameterization, suitable for diffractive configurations and highly tolerant to random noise was developed. The proposed technique can be applied to new characterization tools with high spatial resolution, fast data acquisition, and artificial intelligence, such as high-speed nanoscale metrology and quality control, and can be further developed to high-resolution spectroscop

Diversity Data Explorer - The New Wave Exhibition, Waikato Museum

This project used free census demographic data to create an interactive data visualization. The visualisation allowed users to select data sets on a touch screen which were then projected as coloured bar graphs onto the rooftops of a miniature suburb. Two graphs were selectable and were always compared the the data of the city as a whole. The work was created in collaboration with Simon Nicholls. The projection screen was actually a three dimensional miniature suburb created using 3d modelling and laser cut sculptures

TraitLab: a Matlab package for fitting and simulating binary tree-like data

TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits are simultaneously lost while new ones arise, and borrowing, whereby traits transfer laterally between species as well as through ancestral relationships. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distribution for tree topologies, clade and root ages, and the trait loss, catastrophe and borrowing rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for heterogeneity in the trait loss rate, biases in the data collection process and borrowing of traits between lineages. Coupled pairs of Markov chains can be used to diagnose MCMC mixing and convergence and to debias MCMC estimators. The raw data, MCMC run output, and model fit can be inspected using a number of useful graphical and analytical tools provided within the package or imported into other popular analysis programs. TraitLab is freely available and runs within the Matlab computing environment with its Statistics and Machine Learning toolbox, no other additional toolboxes are required.Comment: Manual describing the TraitLab software for phylogenetic inferenc

Confidence in the face of risk: the Risk Assessment and Management Self-Efficacy Study (RAMSES).

Aims and method To evaluate a comprehensive risk management programme. A Risk Assessment and Management Self-Efficacy Scale (RAMSES) was used to evaluate the impact of a clinical guideline and training course. Fifty-three psychological therapists were randomly allocated to training v. waiting list in a controlled, delayed-intervention design. Differences in mean self-efficacy scores between groups were examined using analysis of covariance (ANCOVA). Results The RAMSES measure had adequate factor structure, internal consistency and construct validity. When adjusting for baseline scores and cluster design, the group exposed to training had a higher mean self-efficacy score than controls. Mean differences between groups were not significant after the control group received training, nor at 6 months' follow-up. Clinical implications Exposure to training and clinical guidelines can improve self-efficacy in risk assessment and management. An important advance put forward by this study is the specification of areas of competence in risk assessment and management, which can be measured using a psychometrically sound tool

Maintaining prostate contouring consistency following an educational intervention

IntroductionThe aim of this study was to assess variation in prostate contouring 12 months following a structured interactive educational intervention (EI) and to test the hypothesis that EIs positively impact on prostate contouring accuracy and consistency long term

Optimizing CRE and PhiC31 mediated recombination in Aedes aegypti

Introduction: Genetic manipulation of Aedes aegypti is key to developing a deeper understanding of this insects’ biology, vector-virus interactions and makes future genetic control strategies possible. Despite some advances, this process remains laborious and requires highly skilled researchers and specialist equipment.Methods: Here we present two improved methods for genetic manipulation in this species. Use of transgenic lines which express Cre recombinase and a plasmid-based method for expressing PhiC31 when injected into early embryos.Results: Use of transgenic lines which express Cre recombinase allowed, by simple crossing schemes, germline or somatic recombination of transgenes, which could be utilized for numerous genetic manipulations. PhiC31 integrase based methods for site-specific integration of genetic elements was also improved, by developing a plasmid which expresses PhiC31 when injected into early embryos, eliminating the need to use costly and unstable mRNA as is the current standard.Discussion: Here we have expanded the toolbox for synthetic biology in Ae. aegypti. These methods can be easily transferred into other mosquito and even insect species by identifying appropriate promoter sequences. This advances the ability to manipulate these insects for fundamental studies, and for more applied approaches for pest control

Qualitative Analysis of the Factors Associated with Whistleblowing Intentions among Athletes from Six European Countries

Although whistleblowing is thought to represent an effective mechanism for detecting and uncovering doping in sport, it has yet to become a widely adopted practice. Understanding the factors that encourage or discourage whistleblowing is of vital importance for the promotion of this practice and the development of pedagogical material to enhance the likelihood of whistleblowing. The current study employed a qualitative methodology to explore the personal and organisational factors that underpin intentions to blow the whistle or that may lead to engagement in whistleblowing behaviours in sport. Thirty-three competitive athletes across a range of sports took part in a semi-structured interview which sought to explore what they would do should they encounter a doping scenario. Content analysis revealed that whistleblowing is a dynamic process characterised by the interaction of a range of personal and organisational factors in determining the intention to report PED use. These factors included moral reasoning, a desire to keep the matter "in-house", perceived personal costs, institutional attitudes to doping, and social support. Analysis revealed a number of 'intervening events' (Ajzen, 1991), including a perceived lack of organisational protection (e.g., ethical leadership) within some sporting sub-cultures, which present an important obstacle to whistleblowing. The intention to report doping was underpinned by a "fairness loyalty trade-off" which involved athletes choosing to adhere to either fairness norms (which relate to a sense that all people and groups are treated equally) or loyalty norms (which reflect preferential treatment towards an in-group) when deciding whether they would blow the whistle. The promotion of fairness norms that emphasise a group's collective interests might encourage athletes to view whistleblowing as a means of increasing group cohesiveness and effectiveness and thereby increase the likelihood of this practice

Social Goals, Motivational Climate, Discipline and Attitudes of the Student According to Teacher

El objetivo ha sido analizar la relación existente entre el género y la experiencia laboral del profesorado con las metas sociales, el clima motivacional, las estrategias de disciplina y las actitudes hacia la Educación Física. La muestra estaba constituida por 970 chicos y 1032 chicas con edades comprendidas entre los 12-19 años. Se aplicó una batería de test compuesta por el EMSEF (Moreno, González-Cutre, y Sicilia, 2007), el LAPOPECQ (Cervelló, Jiménez, Moya, y Moreno, 2010), la SDSS (Gutiérrez, López, y Ruiz, 2009) y el CAEFP (Gutiérrez y Ruíz, 2009). Se analizaron Modelos Lineales de Regresión Múltiple. En los resultados, solo el tiempo de servicio del docente mantiene significatividad con el clima rendimiento y las razones intrínsecas de disciplina. En cambio, la edad del alumnado es significativa con las metas sociales, y el género con el clima rendimiento, ambas metas, las razones introyectadas y la indiferencia del profesor.The aim was to analyze the relationship between gender and work experience of teachers with social goals, motivational climate, discipline strategies and attitudes toward physical education. The sample consisted of 970 boys and 1032 girls aged 12-19. A battery of tests consisting of the EMSEF (Moreno, González-Cutre, and Sicilia, 2007), the LAPOPECQ (Cervelló, Jiménez, Moya, and Moreno, 2010), the SDSS (Gutiérrez, López, and Ruiz, 2009) was applied and CAEFP (Gutiérrez and Ruiz, 2009). Linear Regression Models were analyzed. In the results, only the service time faculty holds significance with performance climate and intrinsic reasons of discipline. In contrast, the age of students is significant to social goals, and gender with performance climate, both goals, introjected reasons and indifference of the teacher

Description and evaluation of the UKCA stratosphere-troposphere chemistry scheme (StratTrop vn 1.0) implemented in UKESM1

Abstract. Here we present a description of the UKCA StratTrop chemical mechanism, which is used in the UKESM1 Earth system model for CMIP6. The StratTrop chemical mechanism is a merger of previously well-evaluated tropospheric and stratospheric mechanisms, and we provide results from a series of bespoke integrations to assess the overall performance of the model. We find that the StratTrop scheme performs well when compared to a wide array of observations. The analysis we present here focuses on key components of atmospheric composition, namely the performance of the model to simulate ozone in the stratosphere and troposphere and constituents that are important for ozone in these regions. We find that the results obtained for tropospheric ozone and its budget terms from the use of the StratTrop mechanism are sensitive to the host model; simulations with the same chemical mechanism run in an earlier version of the MetUM host model show a range of sensitivity to emissions that the current model does not fall within. Whilst the general model performance is suitable for use in the UKESM1 CMIP6 integrations, we note some shortcomings in the scheme that future targeted studies will address. NERC (NE/M00273X/1), NERC (NE/P016383/1), National Centre for Atmospheric Science (NERC) (via University of Leeds) (R8/H12/83/003