Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming

Optimal string alignment is used to discover evolutionary relationships or mutations in DNA/RNA or protein sequences. Errors, missing parts or uncertainty in such a sequence can be covered with wild cards, so-called wild bases. This makes an alignment possible even when the data are corrupted or incomplete. The extended pairwise local alignment of wild card DNA/RNA sequences requires additional calculations in the dynamic programming algorithm and necessitates a subsequent best- and worst-case analysis for the wild card positions. In this paper, we propose an algorithm which solves the problem of input data wild cards, offers a highly flexible set of parameters and displays a detailed alignment output and a compact representation of the mutated positions of the alignment. An implementation of the algorithm can be obtained at https://github.com/sysbio-bioinf/swat+ and http://sysbio.uni-ulm.de/?Software:Swat+.     

The contingent nature of best practices in national competitiveness: The case of American and Japanese innovation processes

We propose that the differences in competitiveness of companies from different countries is not just a question of the adoption of ‘better’ management models, as conventional wisdom would have us believe; rather, we contend that national competitiveness can change radically over time without significant changes in management practices. Contrary to much of the management literature we hold that changes in the global business environment often determine to a large degree the competitiveness of companies. Based on our assumptions we offer four specific lessons of how companies can increase their competitiveness within the constraints of the socio-cultural context in which they operate.     

Perception vs. Circumstances of the Child Sexual Abuse Event in Relation to Depression and Post-traumatic Stress Symptomatology

The study examined the impact of the circumstances of childhood sexual abuse on post-traumatic stress symptoms and depression among female adult survivors of childhood sexual abuse. The sample consisted of 225 Israeli women divided into two groups according to the identity of the perpetrator (nonfamily perpetrator versus a family member perpetrator). A self-report questionnaire was used consisting of the following scales: demographic variables, the Traumatic Events Questionnaire, Childhood Sexual Experiences Scale, Post-Traumatic Stress Disorder Symptom Scale, and Depression Scale. The findings indicated that the identity of the offender significantly differed between groups only if intercourse had occurred. Women who experienced coerced intercourse scored significantly higher on depression and post-traumatic stress compared to those who experienced other forms of childhood sexual abuse.     

Book Review

Affective forecasting refers to the process of predicting emotional reactions to future events. It plays an important role in decision making, but is also prone to errors, such as the ‘impact bias’: a tendency to overestimate the intensity of future reactions. The impact bias has been considered evolutionarily adaptive, as it performs a protective function in motivating people to avoid risky behaviour. Affective forecasting may be qualitatively different in a risk-taking population such as problem gamblers (PGs). In particular, PGs may fail to show the impact bias. This study was the first to examine affective forecasting in PGs. PGs (N = 25) and controls (N = 29) were asked to predict how they would feel after completing a guessing task. As hypothesized, controls exaggerated how bad they would feel after losing at the task, whereas PGs accurately predicted their reactions. Encouraging PGs to focus on anticipated emotions may be a novel target for treatment interventions.     

Leisure Time in Modern Societies: A New Source of Boredom and Stress?

The increase in leisure time over the last century is well documented. We know much less, however, about the quality of the use of leisure time. Quite divergent predictions exist in this regard: Some authors have argued that the new, extensive free time will lead to new forms of time pressure and stress; others have foreseen an expansion of boredom. This is the first paper that systematically investigates the quality of leisure time in 36 countries around the world. It uses the 2007 ISSP-survey “Leisure Time and Sport”. We investigate stress and boredom during leisure time by making use of four general theories about international and intercultural differences. The theories relate to the level of socio-economic development, religious–cultural systems, types of welfare states, and to the emergence of specific “time regimes”. In addition, we control for the effect of relevant individual level variables. At the macro level, significant differences emerge concerning the level of development, the dominant religion, and the extent of welfare benefits. The most interesting finding, however, was that a typology of leisure time regimes is the most suited to explain the considerable differences between the 36 countries compared. Implications of this finding for time policy and further research are discussed in the concluding section.     

Conflict in foreign subsidiaries of Japanese and western multinational corporations: The impact of cultural distance and differences in home-host country combinations

This article investigates the degree of conflict between different groups of employees in MNC subsidiaries in relation to different home-host country combinations. More specifically, we compared the degree of conflict of Western subsidiaries in Japan and Japanese subsidiaries in the West. We based our comprehensive investigation on data from 617 US and German subsidiaries in Japan as well as Japanese subsidiaries in the USA and Germany (and, for comparative reasons, US subsidiaries in Germany and German subsidiaries in the US). Possibly rather surprisingly, our results indicate that different degrees of cultural distance between home and host country do not lead to different degrees of conflict in MNC subsidiaries. We suggest that expected conflicts, due to substantial cultural differences, induce employees to actively counteract such problems, leading ultimately to a reduction of real conflicts. Furthermore, while previous literature suggested that in particular Japanese subsidiaries in the West are prone to a high degree of conflicts, our findings suggest that Western subsidiaries in Japan are even more conflict-laden. This should caution Western companies against complacency when operating in Japan.     

Internationale Mobilit?t und soziale Selektivit?t: Ausma?, Mechanismen und Entwicklung herkunftsspezifischer Unterschiede zwischen 1990 und 2005

In the course of educational expansion social inequalities in access to upper secondary education declined, while the differences in transition to tertiary education increased. In the light of these changes the assumption arises, that the patterns of social selectivity in access to higher education have changed. While in the past status maintenance was mainly due to differences in access to higher education, today it is to a greater extent a question of kind and place of study. Because of the growing importance of international experience for labour market success, students of privileged classes might increasingly opt to study abroad in order to preserve their privileged position. Drawing on a series of panel-datasets of upper secondary graduates in Germany, we estimate the extent and development of social differences in international mobility behaviour between 1990 and 2005, and apply a decomposition method in order to single out the underlying processes and mechanisms. We find remarkable social differences in the intention as well as in the decision to study at a foreign university. Students from privileged classes more often decide to study abroad, while students from underprivileged classes stay close to their hometown. These differences can partly be explained by school performance, language skills, social costs and institutional differences. Furthermore we find that these differences have rather increased than decreased.     

A new monotonic, clone-independent, reversal symmetric, and condorcet-consistent single-winner election method

In recent years, the Pirate Party of Sweden, the Wikimedia Foundation, the Debian project, the “Software in the Public Interest” project, the Gentoo project, and many other private organizations adopted a new single-winner election method for internal elections and referendums. In this article, we will introduce this method, demonstrate that it satisfies, e.g., resolvability, Condorcet, Pareto, reversal symmetry, monotonicity, and independence of clones and present an O(C^3) algorithm to calculate the winner, where C is the number of alternatives.