Statistical and Combinatorial Aspects of Comparative Genomics*

Abstract. This document presents a survey of the statistical and combinatorial aspects of four areas of comparative genomics: gene order based measures of evolutionary distances between species, construction of phylogenetic trees, detection of horizontal transfer of genes, and detection of ancient whole genome duplications.     

Hierarchical likelihood approach to non-Gaussian factor analysis

Factor models, structural equation models (SEMs) and random-effect models share the common feature that they assume latent or unobserved random variables. Factor models and SEMs allow well developed procedures for a rich class of covariance models with many parameters, while random-effect models allow well developed procedures for non-normal models including heavy-tailed distributions for responses and random effects. In this paper, we show how these two developments can be combined to result in an extremely rich class of models, which can be beneficial to both areas. A new fitting procedures for binary factor models and a robust estimation approach for continuous factor models are proposed.     

Learning discrete decomposable graphical models via constraint optimization

Statistical model learning problems are traditionally solved using either heuristic greedy optimization or stochastic simulation, such as Markov chain Monte Carlo or simulated annealing. Recently, there has been an increasing interest in the use of combinatorial search methods, including those based on computational logic. Some of these methods are particularly attractive since they can also be successful in proving the global optimality of solutions, in contrast to stochastic algorithms that only guarantee optimality at the limit. Here we improve and generalize a recently introduced constraint-based method for learning undirected graphical models. The new method combines perfect elimination orderings with various strategies for solution pruning and offers a dramatic improvement both in terms of time and memory complexity. We also show that the method is capable of efficiently handling a more general class of models, called stratified/labeled graphical models, which have an astronomically larger model space.     

A Proportional Hazards Regression Model for the Subdistribution with Covariates‐adjusted Censoring Weight for Competing Risks Data

With competing risks data, one often needs to assess the treatment and covariate effects on the cumulative incidence function. Fine and Gray proposed a proportional hazards regression model for the subdistribution of a competing risk with the assumption that the censoring distribution and the covariates are independent. Covariate‐dependent censoring sometimes occurs in medical studies. In this paper, we study the proportional hazards regression model for the subdistribution of a competing risk with proper adjustments for covariate‐dependent censoring. We consider a covariate‐adjusted weight function by fitting the Cox model for the censoring distribution and using the predictive probability for each individual. Our simulation study shows that the covariate‐adjusted weight estimator is basically unbiased when the censoring time depends on the covariates, and the covariate‐adjusted weight approach works well for the variance estimator as well. We illustrate our methods with bone marrow transplant data from the Center for International Blood and Marrow Transplant Research. Here, cancer relapse and death in complete remission are two competing risks.     

Intensive management reduces butterfly diversity over time in urban green spaces

Urban Ecosystems - Loss and fragmentation of semi-natural grasslands have had negative consequences for grassland biodiversity, such as butterflies. Urban parks and other urban green spaces have so...     

The Shifting Meanings of Popular Engagement in Swedish Society

VOLUNTAS: International Journal of Voluntary and Nonprofit Organizations - The aim of this article is to contribute to the Swedish debate on popular engagement by studying changes in popular...     

100 key research questions for the post‐2015 development agenda

The Sustainable Development Goals (SDGs) herald a new phase for international development. This article presents the results of a consultative exercise to collaboratively identify 100 research questions of critical importance for the post‐2015 international development agenda. The final shortlist is grouped into nine thematic areas and was selected by 21 representatives of international and non‐governmental organisations and consultancies, and 14 academics with diverse disciplinary expertise from an initial pool of 704 questions submitted by 110 organisations based in 34 countries. The shortlist includes questions addressing long‐standing problems, new challenges and broader issues related to development policies, practices and institutions. Collectively, these questions are relevant for future development‐related research priorities of governmental and non‐governmental organisations worldwide and could act as focal points for transdisciplinary research collaborations.     

Comparing swimsuits in 3D

In competitive swimming, suits have become more important. These suits influence friction, pressure and wave drag. Friction drag is related to the surface properties whereas both pressure and wave drag are greatly influenced by body shape. To find a relationship between the body shape and the drag, the anthropometry of several world class female swimmers wearing different suits was accurately defined using a 3D scanner and traditional measuring methods. The 3D scans delivered more detailed information about the body shape. On the same day the swimmers did performance tests in the water with the tested suits. Afterwards the result of the performance tests and the differences found in body shape was analyzed to determine the deformation caused by a swimsuit and its effect on the swimming performance. Although the amount of data is limited because of the few test subjects, there is an indication that the deformation of the body influences the swimming performance.     

Participation for children exposed to domestic violence? Social workers' approaches and children's strategies

This article explores social workers' approaches to children exposed to domestic violence and children's strategies in encounters with these professionals in the context of family law proceedings. Investigator approaches as well as child strategies are reconstructed from children's narratives. Furthermore, possible links between the social worker's approach described by a particular child, and the child's own strategies are outlined. Participation can offer children validation of their experiences and support their recovery after exposure to violence. However, it is suggested that it seems to be a challenging task for social workers to both validate children's experiences of violence and simultaneously offer them participation in the investigation process.