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.     

Creating a reference to a complex emergency situation using time series methods: war in Guinea-Bissau 1998-1999

Impacts of complex emergencies or relief interventions have often been evaluated by absolute mortality compared to international standardized mortality rates. A better evaluation would be to compare with local baseline mortality of the affected populations. A projection of population-based survival data into time of emergency or intervention based on information from before the emergency may create a local baseline reference. We find a log-transformed Gaussian time series model where standard errors of the estimated rates are included in the variance to have the best forecasting capacity. However, if time-at-risk during the forecasted period is known then forecasting might be done using a Poisson time series model with overdispersion. Whatever, the standard error of the estimated rates must be included in the variance of the model either in an additive form in a Gaussian model or in a multiplicative form by overdispersion in a Poisson model. Data on which the forecasting is based must be modelled carefully concerning not only calendar-time trends but also periods with excessive frequency of events (epidemics) and seasonal variations to eliminate residual autocorrelation and to make a proper reference for comparison, reflecting changes over time during the emergency. Hence, when modelled properly it is possible to predict a reference to an emergency-affected population based on local conditions. We predicted childhood mortality during the war in Guinea-Bissau 1998-1999. We found an increased mortality in the first half-year of the war and a mortality corresponding to the expected one in the last half-year of the war.     

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.     

Comparative Journalism Research – An Overview

This overview focuses on the most common type of comparative journalism research, which is cross‐national comparative research. The overview presents a typology for different types of comparative journalism research, based on whether the research interest is in journalism as an activity or as a product; and, in the case of journalism as an activity, whether the interest is in the system level, the organizational level, or the individual level of journalism. The overview finds that the analysis of journalism on the individual level and of journalism as a product are the most common types of comparative research, whereas comparative analysis of journalism on the organizational level is much under‐studied.     

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.     

Decision model for product rollover in manufacturing operations

The purpose of this study is to investigate critical decisions when planning for product rollover at a manufacturing company, and how to organise these decisions. A literature review and a case study are used to develop a decision model. The findings indicate that product rollover can be organised in a five-phase decision model. The research quality is strengthened by a structured literature review, but it can be argued that more empirical research is needed for validation. For researchers, this paper contributes with the identification of critical decisions and a model for product rollover. For practitioners, the study highlights the need to acknowledge the importance of product rollover and its role as a competitive weapon. In earlier studies, product rollover has mainly been investigated from a market perspective, so that this study contributes by investigating the issue from a manufacturing perspective.     

Robust Poisson likelihood estimation for frailty Cox models: A simulation study

Frailty models can be fit as mixed-effects Poisson models after transforming time-to-event data to the Poisson model framework. We assess, through simulations, the robustness of Poisson likelihood estimation for Cox proportional hazards models with log-normal frailties under misspecified frailty distribution. The log-gamma and Laplace distributions were used as true distributions for frailties on a natural log scale. Factors such as the magnitude of heterogeneity, censoring rate, number and sizes of groups were explored. In the simulations, the Poisson modeling approach that assumes log-normally distributed frailties provided accurate estimates of within- and between-group fixed effects even under a misspecified frailty distribution. Non-robust estimation of variance components was observed in the situations of substantial heterogeneity, large event rates, or high data dimensions.     

Overcoming the Glass Barriers: Reflection and Action in the ‘Women to the Top’ Programme

Numerous equality programmes have been launched with the aim of promoting a more gender equal work life, yet little substantial action has been reported. This article presents a study of the Women to the Top programme in Sweden, supported by the European Union (EU) and aimed at promoting more women into top management positions. The research suggests that large‐scale projects assembling such heterogeneous actors as industry representatives, politicians and scholars tend to generate further reflection and discussion rather than promoting adequate and highly needed action. Drawing upon Brunsson's distinction between action rationality and decision rationality, the relatively modest effects of large‐scale equality programmes are examined, not in terms of a lack of commitment or competence on the part of the participants but as a matter of the disjunction between reflection and action. Reconciling reflection and action, that is, emphasizing not only reflection on gender inequality but also privileging various forms of practical action (such as new policies, the appointment of female managers, restructuring gendered wage inequalities or new recruitment procedures), is therefore a top priority for policymakers desiring more substantial changes in the gendered outline of industry.     

The satisfaction of Finnish adoptive parents with statutory pre-adoption counselling in inter-country adoptions

We examined how satisfied Finnish adoptive parents were with statutory pre-adoption counselling in inter-country adoptions. The data were collected through the Finnish Adoption Study using a retrospective survey measuring satisfaction with received pre-adoption counselling. All adoptive parents with a child under the age of 18, adopted from abroad between the years 1990 and 2007, were included. The sample of the study comprised parents of 1451 children and a total response rate of 55.7% was achieved. The data consisted of self-scored reports of satisfaction as well as open answer questions. Parent satisfaction and associated variables were analysed using chi-square and multiple logistic regression. Of the respondents, 81.7% reported satisfaction with the pre-adoption counselling they had received. The level of satisfaction was stable over time and did not differ according to service provider, whereas family type and sending country were associated with satisfaction. However the explanations for satisfaction were different for those services provided in units specialized in adoption and for those provided by municipal child protection services. The components found to explain satisfaction and dissatisfaction were experience, adoption knowledge, and attitude of the social worker, service accessibility and availability issues, as well as the content of the pre-adoption counselling offered.