Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.

School Bullies’ Quest for Power: Implications for Group Dynamics and Intervention

Bullying is characterized by an inequality of power between perpetrator and target. Findings that bullies can be highly popular have helped redefine the old conception of the maladjusted school bully into a powerful individual exerting influence on his peers from the top of the peer status hierarchy. Study I is a conceptual paper that explores the conditions under which a skillful, socially powerful bully can use the peer group as a means of aggression and suggests that low cohesion and low quality of friendships make groups easier to manipulate. School bullies’ high popularity should be a major obstacle for antibullying efforts, as bullies are unlikely to cease negative actions that are rewarding, and their powerful position could discourage bystanders from interfering. Using data from the Finnish program KiVa, Study II supported the hypothesis that antibullying interventions are less effective with popular bullies in comparison to their unpopular counterparts. In order to design interventions that can address the positive link between popularity and aggression, it is necessary to determine in which contexts bullies achieve higher status. Using an American sample, Study III examined the effects of five classroom features on the social status that peers accord to aggressive children, including classroom status hierarchy, academic level and grade level, controlling for classroom mean levels of aggression and ethnic distribution. Aggressive children were more popular and better liked in fifth grade relative to fourth grade and in classrooms of higher status hierarchy. Surprisingly, the natural emergence of status hierarchies in children’s peer groups has long been assumed to minimize aggression. Whether status hierarchies hinder or promote bullying is a controversial question in the peer relations’ literature. Study IV aimed at clarifying this debate by testing the effects of the degree of classroom status hierarchy on bullying. Higher hierarchy was concrrently associated with bullying and predictive of higher bullying six months later. As bullies’ quest for power is increasingly acknowledged, some researchers suggest teaching bullies to attain the elevated status they yearn for through prosocial acts. Study V cautions against such solutions by reviewing evidence that prosocial behaviors enacted with the intention of controlling others can be as harmful as aggression.

The quest for a better understanding of chronic kidney disease complications: an update on uremic toxins

Chronic kidney disease is characterized by a progressive reduction of glomerular filtration rate and/or the appearance of proteinuria, and subsequently the progressive retention of organic waste compounds called uremic toxins (UT). Over the last decades, a large number of such compounds have been identified and their effects on organs and tissues, especially the cardiovascular system, has been demonstrated. In this review, we present the current classification of UT, as proposed by the EUTox Group, and the effects of some of the probably most important UTs, such as phosphate, FGF-23, PTH, AGEs, indoxyl sulfate and para-cresyl sulfate. We provide an overview on therapeutic approaches aimed to increase their extracorporeal removal via convective and/or adsorptive strategies and to lower their intestinal production/ absorption via dietetic and pharmacological interventions. The recognition that multiple toxins contribute to the uremia supports the need for new therapeutic targets, with a potentially positive impact on CKD progression and survival.

Quest/ion of Identities in African American Feminist Postmodern Drama: A Study of Selected Plays by Suzan-Lori Parks

Innovative and unconventional, Pulitzer Prize-winning playwright Suzan-Lori Parks belongs to the continuum of African American playwrights who have contributed to the quest/ion – the quest for and question – of identities for African Americans. Her plays are sites in which the quest/ion of identities for African Americans is pursued, raised and enacted. She makes use of both page and stage to emphasize the exigency of reshaping African Americans’ identities through questioning the dominant ideologies and metanarratives, delegitimizing some of the prevailing stereotypes imposed on them, drawing out the complicity of the media in perpetuating racism, evoking slavery, lynching and their aftereffects, rehistoricizing African American history, catalyzing reflections on the various intersections of sex, race, class and gender orientations, and proffering alternative perspectives to help readers think more critically about issues facing African Americans. In my dissertation, I approach three plays by Parks – The Death of the Last Black Man in the Whole Entire World (1990), Venus (1996) and Fucking A (2000) – from the standpoints of postmodern drama and African American feminism with a focus on the terrains that reflect the quest/ion of identities for African Americans, especially African American women. I argue that postmodern drama and African American feminism provide the ground for Parks to promote the development of a political agenda in order to call into question a number of dominant ideologies and metanarratives with regard to African Americans and draw upon the roles of those metanarratives as a powerful apparatus of racial and sexual oppressions. I also explore how Parks engages with postmodern drama and African American feminism to incorporate her own mininarratives in the dominant discourses. I argue that Parks in these plays uses postmodern drama and African American feminism to encourage reflections on intersectionality in order to reveal the concerns of African Americans, particularly African American women. Her plays challenge the dominant order of hierarchy and patriarchy, while in some cases urging unity and solidarity between African American men and women by showing how unity and solidarity can help them confront race, class and gender oppressions. Furthermore, I discuss how the utilization of postmodern techniques and devices helps Parks to transform the conventional features of playwriting, to create incredulity toward the dominant systems of oppression and to incorporate her mininarratives within the context of dominant discourses.

Itinerario istruttivo di Roma antica e moderna ovvero descrizióne generale dei monumenti antichi e moderni e delle opere le piu insigni dipittura, scultura ed architettura di quest' alma cittae delle sue adiacerze

UANL

The Quest for Hegemony Among Countries and Global Pollution

This paper builds on the assumption that countries behave in such a way as to improve, via their economic strength, the probability that they will attain the hegemonic position on the world stage. The quest for hegemony is modeled as a game, with countries being differentiated initially only by some endowment which yields a pollution free flow of income. A country's level of pollution is assumed directly related to its economic strength, as measured by its level of production. Two types of countries are distinguished: richly-endowed countries, for whom the return on their endowment is greater than the return they can expect from winning the hegemony race, and poorly-endowed countries, who can expect a greater return from winning the race than from their endowment. We show that in a symmetric world of poorly-endowed countries the equilibrium level of emissions is larger than in a symmetric world of richly-endowed countries: the former, being less well endowed to begin with, try harder to win the race. In the asymmetric world composed of both types of countries, the poorly-endowed countries will be polluting more than the richly endowed countries. Numerical simulations show that if the number of richly-endowed countries is increased keeping the total number of countries constant, the equilibrium level of global emissions will decrease; if the lot of the poorly-endowed countries is increased by increasing their initial endowment keeping that of the richly-endowed countries constant, global pollution will decrease; increasing the endowments of each type of countries in the same proportion, and hence increasing the average endowment in that proportion, will decrease global pollution; redistributing from the richly-endowed in favor of the poorly-endowed while keeping the average endowment constant will in general result in an increase in the equilibrium level of global pollution.

Believing in belief : the modernist quest for spiritual meaning (Croyer en croyance : la quête moderniste pour le sens spirituel)

Cette thèse défend l’idée que plusieurs auteurs modernistes ont utilisé des concepts centraux à la croyance religieuse traditionnelle afin de préconiser le changement social. Au lieu de soutenir l'hypothèse de la sécularisation, qui prétend que les modernistes ont rejeté la religion en faveur d'une laïcité non contestée, j'argumente en faveur de ce que j'appelle « la spiritualité moderniste, » qui décrie une continuité intégrale des concepts spirituels dans l'agitation de la période moderniste qui a déstabilisée les institutions qui avait auparavant jeté les bases de la société Occidentale. En me basant sur les écrit de Sigmund Freud, William James et Émile Durkheim concernant les fins poursuivis par la religion, je développe cinq concepts centraux de la croyance religieuse que les modernistes ont cherché à resignifier, à savoir la rédemption, la communauté, la sacralité, le spectre, et la liturgie, et, dans chaque cas, j'ai montré comment ces catégories ont été réinterprétées pour traiter des questions considérées comme essentielles au début du vingtième siècle, à savoir ce que l’on identifie aujourd’hui comme le féminisme, l'écologie, la biopolitique, les crises, et le rôle du poète. Le chapitre I se concentre sur la rédemption par le féminin telle qu’on la trouve dans le recueil de vers de H.D. portant sur la Seconde Guerre mondiale, Trilogy (1944-1946), qui projette un certain espoir grâce à un mélange synchrétique de Christianisme, de mythes anciens, d’astrologie, et de psychologie. Mon deuxième chapitre discute de The Grapes of Wrath (1939) de John Steinbeck, qui élargit le rôle de la communauté en avançant une écologie universelle qui concevoit tous les gens comme étant intimement liés entre eux et avec le monde. Le chapitre III traite de la notion du sacré dans The Light in August (1932) de Willam Faulkner et Nightwood (1936) de Djuna Barnes, qui préconisent une foi privatisée qui accentue l'illégitimité des concepts de sacralité et de pollution en élevant des individus qui sont marginalisés biopolitiquement. Le chapitre IV cherche à comprendre le retour des morts, et je soutiens que le topos a été utilisé par les modernistes comme un symbole de crises sociales; le chapitre enquête d'abord sur “The Jolly Corner” (1908) de Henry James, que j'ai lu comme la séquence rêvée d'un homme faisant face à son propre spectre, Ulysses (1922) de James Joyce, où Stephen Dedalus est hanté de façon répétée par le spectre de sa mère, et Mrs. Dalloway (1925) de Virginia Woolf, qui se concentre sur le motif caché de la Fête des Morts. Ma cinquième section traite de la liturgie, la langue poétique utilisée pour les rites religieux, dans la première poésie de Wallace Stevens, qui conçoit le rôle du poète comme une vocation de l'imagination.