On Tree Pattern Matching by Pushdown Automata

Tree pattern matching is an important operation in Computer Science on which a number of tasks such as mechanical theorem proving, term-rewriting, symbolic computation and non-procedural programming languages are based on. Work has begun on a systematic approach to the construction of tree pattern matchers by deterministic pushdown automata which read subject trees in prefix notation. The method is analogous to the construction of string pattern matchers: for given patterns, a non-deterministic pushdown automaton is created and then it is determinised. In this first paper, we present the proposed non-deterministic pushdown automaton which will serve as a basis for the determinisation process, and prove its correctness.

Systematic errors in phylogenetic trees

The effort to reconstruct the tree of life was revolutionized by the use of sequences of proteins and nucleic acids. Phylogenetic trees are now routinely inferred using hundreds of thousands of amino acid or nucleotide characters. It thus seems surprising that many aspects of the tree of life are still controversial; conflicting results between large scale phylogenomic studies show that errors remain common despite large datasets. These errors often result from systematic biases in the way sequences evolve. While the resulting systematic errors are well understood, it requires careful efforts to reduce their effects

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations

The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the PLF currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation

The role of inflammation in the association between poverty and working memory in childhood

Background: Family financial difficulties have been directly linked to poorer executive functioning in childhood. However, recent studies suggest that difficulties in affording basic items and other necessities may also indirectly affect children’s executive functions through several psychological but also physiological paths. One of the latter may be inflammation, which has been related to both financial difficulties and executive functioning. In this study, we explored for the first time if the relationship between early family financial difficulties and working memory in middle childhood can be explained by inflammation. / Methods: Using data from 4,525 children of the Avon Longitudinal Study of Parents and Children, a general population birth cohort, we tested associations between parents’ perceptions at ages 0-3 years of having difficulties in affording basic items for their children including food and clothing, and children’s inflammation [measured by interleukin 6 (IL-6) and C-reactive protein (CRP)] at age 9 years and working memory performance at age 10 years. Confounders included socioeconomic status at ages 0-3 years, economic hardship between ages 3-9 years, BMI and gender. / Results: Using Structural Equation Modelling, we found that financial difficulties were associated with worse working memory (β=-0.076, 95% CI=-0.105, -0.043) even after adjusting for confounders. This association was partially explained by inflammation (β=-0.002, 95% CI=-0.005, -0.001) as measured by IL-6. / Conclusions: Children in families struggling to afford necessities early in life have higher levels of inflammation, in turn related to poorer executive functioning in middle childhood. These findings suggest that living under financial strain has a unique effect on children’s cognitive development through inflammation in the general population

Do upsetting life events explain the relationship between low socioeconomic status and systemic inflammation in childhood? Results from a longitudinal study

BACKGROUND Children from families of low socioeconomic status (SES) are more likely to be exposed to upsetting situations and stressors. Such exposures have, in turn, been linked to inflammation in some studies. In this study we explore if low SES is related to inflammation in children via such stressful life events. METHODS Data on 4,525 children of the Avon Longitudinal Study of Parents and Children, a general population birth cohort, were used to explore associations between SES at ages 0-3 years, upsetting life events at ages 3-9 years and inflammatory markers [interleukin 6 (IL-6) and C-reactive protein (CRP)] at age 9 years. Confounders included body mass index, gender, financial problems, and upsetting life events at ages 0-3 years. RESULTS Using Structural Equation Modelling, we found that early socioeconomic disadvantage predicted higher levels of IL-6 (β=0.034, 95% CI=0.063, 0.005) even after adjusting for confounders. This association was partially mediated by upsetting life events (β=0.003, 95% CI=0.011, 0.001). CONCLUSIONS In the general child population, low SES is associated with increased exposure to stressful life events, in turn associated with later inflammation. These findings highlight the role of stressors associated with poverty and disadvantage in the development of inflammation among children in the general population

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here, we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multilocus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general, the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real data sets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative. [BPP; introgression; multispecies coalescent; phase; species tree.

Parent-Child Communication About Educational Aspirations: Experiences of Adolescents in Rural China

The importance of parents in the transmission of educational aspirations to children is well-established. However, little is known about the quality of parent-child communication about educational aspirations and how this communication relates to children’s educational aspirations in socioeconomically disadvantaged families in rural China. In this study, we sought to gain insight into parent-child communication around educational aspirations from the perspective of Chinese rural adolescents. Twenty-three grade-9 students were recruited from middle schools in Songzi, a poor rural county in central China. Participants comprised 12 boys and 11 girls aged 14 to 16 years (M = 14.65 years, SD = 0.59). Students completed one-to-one qualitative interviews about parent-child communication and their educational aspirations in June 2020. Thematic analysis revealed that adolescents’ educational aspirations were strongly influenced by their parents’ beliefs and aspirations for them, with fulfilling parental aspirations and achieving economic success being important influences on rural adolescents’ educational aspirations. However, parent-child communication quality was undermined when parents had an authoritarian communication style and when parents were absent due to rural-urban migration, in which case adolescents reported stress and perceived lack of support in achieving their goals. In addition, mothers were viewed as playing a more vital role in communication than fathers. The implications of the findings for school and community-based interventions promoting rural parents’ ability to communicate effectively with their children about academic concerns are discussed

Outdoor and indoor air quality and cognitive ability in young children

BACKGROUND: This study examined outdoor and indoor air quality at ages 9 months and 3 years and their association with cognitive ability at age 3 in England and Wales. METHOD: Data from 8198 Millennium Cohort Study children were analysed using multilevel regression. Outdoor air quality was assessed with mean annual estimates of nitrogen dioxide (NO2) levels within a standard small area (ward). Indoor air quality was measured with parent-reports of damp or condensation in the home and exposure to secondhand smoke in the home. Cognitive ability was assessed with the British Ability Scales Naming Vocabulary subscale and the Bracken School Readiness Assessment. RESULTS: In adjusted models, consistent exposure to high levels of NO2 at age 9 months and age 3 years was associated with lower verbal ability at age 3 years. Damp/condensation and secondhand smoke in the home at either age or at both ages were correlated with lower school readiness at age 3 years. Exposures to damp/condensation at age 3 years or at both ages and secondhand smoke at either age or at both ages were associated with lower verbal ability at age 3 years. CONCLUSION: Young children's exposures to indoor damp or condensation and secondhand smoke are likely to be detrimental for their cognitive outcomes. However, there do not appear to be any short-term effects of NO2

The State of Software for Evolutionary Biology

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/Cþþ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software developmen

Does general intelligence moderate the association between inflammation and psychological distress?

Research has shown that inflammation is implicated in the pathogenesis of mental health disorders, but not all individuals with such disorders have raised inflammatory markers. This study examined whether general intelligence may be a protective factor for 9666 adults aged 18–97 with elevated inflammation, measured with C-reactive protein (CRP), using data from the UK's Understanding Society. In multigroup analyses for males and females, multiple linear regression was used to model psychological distress dependent upon CRP, adjusting for a host of possible confounders including alcohol consumption, smoking status, history of cardiovascular disease or diabetes, physical exercise and obesity. Moderation by intelligence was tested with a multiplicative interaction term. Results showed that, in adjusted models, CRP was related to an increase in psychological distress in males (β = .049) but not females. Furthermore, intelligence moderated the effect of CRP on psychological distress in males (β = −.037), such that males with higher CRP levels were at lower risk with increased intelligence. In conclusion, general intelligence may protect male adults from the negative effects of inflammation on psychological distress