Ancestral sequence alignment under optimal conditions

BACKGROUND: Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. RESULTS: We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. CONCLUSION: We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the success of aligning ancestral sequences containing ambiguity is very sensitive to the choice of gap open cost. Surprisingly, we find that using maximum likelihood to infer ancestral sequences results in less accurate alignments than when using parsimony to infer ancestral sequences. Finally, we find that the sum-of-pairs methods produce better alignments than all of the ancestral alignment methods

MaGe: A Monte Carlo framework for the Gerda and Majorana double beta decay experiments

The Gerda [1] and Majorana [2] projects, both searching for the neutrinoless double beta-decay of 76Ge, are developing a joint Monte-Carlo simulation framework called MaGe. Such an approach has many benefits: the workload for the development of general tools is shared between more experts, the code is tested in more detail, and more experimental data is made available for validation

MaGe: a Monte Carlo framework for the Gerda and Majorana double beta decay experiments

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Patterns and universals of mate poaching across 53 nations : the effects of sex, culture, and personality on romantically attracting another person’s partner

As part of the International Sexuality Description Project, 16,954 participants from 53 nations were administered an anonymous survey about experiences with romantic attraction. Mate poaching--romantically attracting someone who is already in a relationship--was most common in Southern Europe, South America, Western Europe, and Eastern Europe and was relatively infrequent in Africa, South/Southeast Asia, and East Asia. Evolutionary and social-role hypotheses received empirical support. Men were more likely than women to report having made and succumbed to short-term poaching across all regions, but differences between men and women were often smaller in more gender-egalitarian regions. People who try to steal another's mate possess similar personality traits across all regions, as do those who frequently receive and succumb to the poaching attempts by others. The authors conclude that human mate-poaching experiences are universally linked to sex, culture, and the robust influence of personal dispositions.peer-reviewe

Are men universally more dismissing than women? Gender differences in romantic attachment across 62 cultural regions

The authors thank Susan Sprecher (USA), Del Paulhus (Canada), Glenn D. Wilson (England), Qazi Rahman (England), Alois Angleitner (Germany), Angelika Hofhansl (Austria), Tamio Imagawa (Japan), Minoru Wada (Japan), Junichi Taniguchi (Japan), and Yuji Kanemasa (Japan) for helping with data collection and contributing significantly to the samples used in this study.Gender differences in the dismissing form of adult romantic attachment were investigated as part of the International Sexuality Description Project—a survey study of 17,804 people from 62 cultural regions. Contrary to research findings previously reported in Western cultures, we found that men were not significantly more dismissing than women across all cultural regions. Gender differences in dismissing romantic attachment were evident in most cultures, but were typically only small to moderate in magnitude. Looking across cultures, the degree of gender differentiation in dismissing romantic attachment was predictably associated with sociocultural indicators. Generally, these associations supported evolutionary theories of romantic attachment, with smaller gender differences evident in cultures with high–stress and high–fertility reproductive environments. Social role theories of human sexuality received less support in that more progressive sex–role ideologies and national gender equity indexes were not cross–culturally linked as expected to smaller gender differences in dismissing romantic attachment.peer-reviewe

As cold as a fish? Relationships between the Dark Triad personality traits and affective experience during the day: A day reconstruction study

The Dark Triad of personality is a cluster of three socially aversive personality traits: Machiavellianism, narcissism and psychopathy. These traits are associated with a selfish, aggressive and exploitative interpersonal strategy. The objective of the current study was to establish relationships between the Dark Triad traits (and their dimensions) and momentary affect. Machiavellianism, grandiose narcissism, vulnerable narcissism and the dimensions of the Triarchic model of psychopathy (namely, boldness, meanness and disinhibition) were examined. We used the Day Reconstruction Method, which is based on reconstructing affective states experienced during the previous day. The final sample consisted of 270 university students providing affective ratings of 3047 diary episodes. Analyses using multilevel modelling showed that only boldness had a positive association with positive affective states and affect balance, and a negative association with negative affective states. Grandiose narcissism and its sub-dimensions had no relationship with momentary affect. The other dark traits were related to negative momentary affect and/or inversely related to positive momentary affect and affect balance. As a whole, our results empirically demonstrated distinctiveness of the Dark Triad traits in their relationship to everyday affective states. These findings are not congruent with the notion that people with the Dark Triad traits, who have a dispositional tendency to manipulate and exploit others, are generally cold and invulnerable to negative feelings. The associations between the Dark Triad and momentary affect were discussed in the contexts of evolutionary and positive psychology, in relation to the role and adaptive value of positive and negative emotions experienced by individuals higher in Machiavellianism, narcissism and psychopathy

Empowerment, stress vulnerability and burnout among portuguese nursing staff

The work environment in Portuguese hospitals, characterized by economic cutbacks, can lead to higher levels of burnout experienced by nursing staff. Furthermore, vulnerability to stress can negatively affect the perception of burnout in the workplace. However, structural empowerment is an organizational process that can prevent and decrease burnout among nurses. Consequently, the aim of the study was to examine to what extent structural empowerment and vulnerability to stress can play a predictive role in core burnout in a sample of Portuguese nurses. A convenience sample of 297 nursing staff members from Portuguese hospitals was used in this study. Core burnout was negatively and significantly related to all the dimensions of structural empowerment, and it was positively and significantly related to vulnerability to stress. Regression models showed that core burnout was significantly predicted by access to funds, access to opportunities and vulnerability to stress. Organizational administrations must make every effort in designing interventions focused on structural empowerment, as well as interventions focused on individual interventions that enhance skills for coping with stress.info:eu-repo/semantics/publishedVersio

Narcissism and the strategic pursuit of short-term mating : universal links across 11 world regions of the International Sexuality Description Project-2.

Previous studies have documented links between sub-clinical narcissism and the active pursuit of short-term mating strategies (e.g., unrestricted sociosexuality, marital infidelity, mate poaching). Nearly all of these investigations have relied solely on samples from Western cultures. In the current study, responses from a cross-cultural survey of 30,470 people across 53 nations spanning 11 world regions (North America, Central/South America, Northern Europe, Western Europe, Eastern Europe, Southern Europe, Middle East, Africa, Oceania, Southeast Asia, and East Asia) were used to evaluate whether narcissism (as measured by the Narcissistic Personality Inventory; NPI) was universally associated with short-term mating. Results revealed narcissism scores (including two broad factors and seven traditional facets as measured by the NPI) were functionally equivalent across cultures, reliably associating with key sexual outcomes (e.g., more active pursuit of short-term mating, intimate partner violence, and sexual aggression) and sex-related personality traits (e.g., higher extraversion and openness to experience). Whereas some features of personality (e.g., subjective well-being) were universally associated with socially adaptive facets of Narcissism (e.g., self-sufficiency), most indicators of short-term mating (e.g., unrestricted sociosexuality and marital infidelity) were universally associated with the socially maladaptive facets of narcissism (e.g., exploitativeness). Discussion addresses limitations of these cross-culturally universal findings and presents suggestions for future research into revealing the precise psychological features of narcissism that facilitate the strategic pursuit of short-term mating