Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

Interrogating eleven fast-evolving genes for signatures of recent positive selection in worldwide human populations

Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs inchimpanzee, mouse, rat and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes were then further explored for signatures of recent positive selection using SNP data. We genotyped 223 SNPs in 39 worldwide populations from the HGDP Diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each gene. After exploring the allele frequency spectrum, population differentiation and the maintainance of long unbroken haplotypes, we found signals of recent adaptative phenomena in only one of the 11 candidate gene regions. However, the signal ofrecent selection in this region may come from a different, neighbouring gene (CD5) ratherthan from the candidate gene itself (VPS37C). For this set of positively-selected genes in thehuman lineage, we find no indication that these genes maintained their rapid evolutionarypace among human populations. Based on these data, it therefore appears that adaptation forhuman-specific and for population-specific traits may have involved different genes.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Computer-simulation study of magnetic relaxation in anisotropic magnetic systems

We present a computer-simulation study of the effect of the distribution of energy barriers in an anisotropic magnetic system on the relaxation behavior of the magnetization. While the relaxation law for the magnetization can be approximated in all cases by a time logarithmic decay, the law for the dependence of the magnetic viscosity with temperature is found to be quite sensitive to the shape of the distribution of barriers. The low-temperature region for the magnetic viscosity never extrapolates to a positive no-null value. Moreover our computer simulation results agree reasonably well with some recent relaxation experiments on highly anisotropic single-domain particles.

Recognition of Gram-positive Intestinal Bacteria by Hybridoma- and Colostrum-derived Secretory Immunoglobulin A Is Mediated by Carbohydrates.

Humans live in symbiosis with 10(14) commensal bacteria among which >99% resides in their gastrointestinal tract. The molecular bases pertaining to the interaction between mucosal secretory IgA (SIgA) and bacteria residing in the intestine are not known. Previous studies have demonstrated that commensals are naturally coated by SIgA in the gut lumen. Thus, understanding how natural SIgA interacts with commensal bacteria can provide new clues on its multiple functions at mucosal surfaces. Using fluorescently labeled, nonspecific SIgA or secretory component (SC), we visualized by confocal microscopy the interaction with various commensal bacteria, including Lactobacillus, Bifidobacteria, Escherichia coli, and Bacteroides strains. These experiments revealed that the interaction between SIgA and commensal bacteria involves Fab- and Fc-independent structural motifs, featuring SC as a crucial partner. Removal of glycans present on free SC or bound in SIgA resulted in a drastic drop in the interaction with Gram-positive bacteria, indicating the essential role of carbohydrates in the process. In contrast, poor binding of Gram-positive bacteria by control IgG was observed. The interaction with Gram-negative bacteria was preserved whatever the molecular form of protein partner used, suggesting the involvement of different binding motifs. Purified SIgA and SC from either mouse hybridoma cells or human colostrum exhibited identical patterns of recognition for Gram-positive bacteria, emphasizing conserved plasticity between species. Thus, sugar-mediated binding of commensals by SIgA highlights the currently underappreciated role of glycans in mediating the interaction between a highly diverse microbiota and the mucosal immune system.

Women in leadership: Three essays

GENDER EMPOWERMENT: EFFECTS OF GODS, GEOGRAPHY, AND GDP¦Fenley, M., & Antonakis, J.¦ABSTRACT¦We examined the determinants of women's empowerment in the economy and political leadership in 178 countries. Given the androcentric nature of most religions, we hypothesized that high degrees of country-level theistic belief create social conditions that impede the progression of women to power. The dependent variable was the Gender Empowerment index of the United Nations Development Program, which captures the participation of women in political leadership, management, and their share of national income. Controlling for GDP per capita as well as the fixed-effects of the dominant type of religion and legal origin and instrumenting all endogenous variables with geographic or historical variables, our results show that atheism has a significant positive effect on gender empowerment. These results are driven by the rule of law, which in addition to being a catalyst for economic development, appears to crowd-out the informal regulation of behavior due to religious norms.¦DEVELOPING WOMEN LEADERS: COMPARING A TRANSFORMATIONAL AND A CHARISMATIC LEADERSHIP INTERVENTION¦Fenley, M., Jacquart, P., & Antonakis, J.¦ABSTRACT¦Along with a gender imbalance in leadership role occupancy, most leadership interventions have been conducted with samples of men. We conducted an experiment wherein we assigned female participants (n = 38, mean age = 35 years) to one of two conditions: Transformational (i.e., "standard") leadership training or charismatic leadership training. The two interventions were essentially equivalent, except that we also focused on developing the "charismatic leadership tactics" (e.g., rhetorical skills) of participants in the charismatic condition. After the interventions, we randomly assigned participants into problem-solving teams that required extensive interaction. Each team had an equal number of participants having received transformational training or charismatic training. At the end of the team exercises, participants rated each of their team members on a leadership prototypicality measure. Results indicated that those who received charismatic training scored higher (a) on prototypicality (standardized  = .42) and (b) on a test of declarative knowledge of charismatic rhetorical strategies (i.e., a manipulation check, standardized  = .76). Furthermore, the score on the test fully mediated the effect of the treatment on prototypicality (standardized indirect  = .32). We discuss the importance and practical implications of these results.¦CHANGING ATTITUDES TOWARDS WOMEN IN A MALE SEX-TYPE WORK ENVIRONMENT: EVIDENCE FROM A FIELD EXPERIMENT IN EUROPEAN ATHLETICS¦Fenley, M.¦ABSTRACT¦Most sports organizations have a similar gender gap in leadership as do the majority of non-sport organizations. Women's careers sputter somewhere at coaching level positions and few women obtain top leadership positions. Greater awareness of gender inequalities in general, and in leadership in particular, could decrease gender discrimination and increase women's presence at upper levels. The goal of this study was to evaluate the impact of an intervention using an online gender awareness exercise. Participants (n = 1,001 participants, n = 32 countries) were randomly assigned to one of eight conditions in a 2 (a discriminating perspective-taking story or a non-discriminating perspective-taking story) by 2 (gender quiz or no gender quiz) by 2 (diversity quiz or no diversity quiz) factorial design. The results show that the online perspective taking exercise changed initial sexist attitudes. Participants having taken a diversity quiz had less sexist attitudes (as measured by the Modern- and Old-fashioned sexism scale) than did participants who did not take the diversity quiz (irrespective of perspective-taking story). The combination of having taken a diversity quiz with a gender quiz had the biggest impact on attitudes for the non-discriminating story.

The Case for Linking World Law Data

The present paper advocates for the creation of a federated, hybrid database in the cloud, integrating law data from all available public sources in one single open access system - adding, in the process, relevant meta-data to the indexed documents, including the identification of social and semantic entities and the relationships between them, using linked open data techniques and standards such as RDF. Examples of potential benefits and applications of this approach are also provided, including, among others, experiences from of our previous research, in which data integration, graph databases and social and semantic networks analysis were used to identify power relations, litigation dynamics and cross-references patterns both intra and inter-institutionally, covering most of the World international economic courts.

Net Neutrality and other challenges for the future of the Internet. Proceedings of the 7th International Conference on Internet, Law & Politics. Universitat Oberta de Catalunya, Barcelona, 11-12 July, 2011

Peer-reviewed

Interpreting Breast International Group (BIG) 1-98: a randomized, double-blind, phase III trial comparing letrozole and tamoxifen as adjuvant endocrine therapy for postmenopausal women with hormone receptor-positive, early breast cancer.

The Breast International Group (BIG) 1-98 study is a four-arm trial comparing 5 years of monotherapy with tamoxifen or with letrozole or with sequences of 2 years of one followed by 3 years of the other for postmenopausal women with endocrine-responsive early invasive breast cancer. From 1998 to 2003, BIG -98 enrolled 8,010 women. The enhanced design f the trial enabled two complementary analyses of efficacy and safety. Collection of tumor specimens further enabled treatment comparisons based on tumor biology. Reports of BIG 1-98 should be interpreted in relation to each individual patient as she weighs the costs and benefits of available treatments. Clinicaltrials.gov ID: NCT00004205.

The complete genome sequence of the gram-positive bacterium Bacillus subtilis.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Asymptotic equivalence between the unconditional maximum likelihood and the square-law nonlinearity symbol timing estimation

This paper provides a systematic approach to theproblem of nondata aided symbol-timing estimation for linearmodulations. The study is performed under the unconditionalmaximum likelihood framework where the carrier-frequencyerror is included as a nuisance parameter in the mathematicalderivation. The second-order moments of the received signal arefound to be the sufficient statistics for the problem at hand and theyallow the provision of a robust performance in the presence of acarrier-frequency error uncertainty. We particularly focus on theexploitation of the cyclostationary property of linear modulations.This enables us to derive simple and closed-form symbol-timingestimators which are found to be based on the well-known squaretiming recovery method by Oerder and Meyr. Finally, we generalizethe OM method to the case of linear modulations withoffset formats. In this case, the square-law nonlinearity is foundto provide not only the symbol-timing but also the carrier-phaseerror.

Positive time-frequency distributions based on joint marginal constraints

This correspondence studies the formulation of members ofthe Cohen-Posch class of positive time-frequency energy distributions.Minimization of cross-entropy measures with respect to different priorsand the case of no prior or maximum entropy were considered. It isconcluded that, in general, the information provided by the classicalmarginal constraints is very limited, and thus, the final distributionheavily depends on the prior distribution. To overcome this limitation,joint time and frequency marginals are derived based on a "directioninvariance" criterion on the time-frequency plane that are directly relatedto the fractional Fourier transform.