PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

On the foundations of well-being economics and policy

When one wishes to implement public policies, there is a previous need of comparing different actions and valuating and evaluating them to assess their social attractiveness. Recently the concept of well-being has been proposed as a multidimensional proxy for measuring societal prosperity and progress; a key research topic is then on how we can measure and evaluate this plurality of dimensions for policy decisions. This paper defends the thesis articulated in the following points: 1. Different metrics are linked to different objectives and values. To use only one measurement unit (on the grounds of the so-called commensurability principle) for incorporating a plurality of dimensions, objectives and values, implies reductionism necessarily. 2. Point 1) can be proven as a matter of formal logic by drawing on the work of Geach about moral philosophy. This theoretical demonstration is an original contribution of this article. Here the distinction between predicative and attributive adjectives is formalised and definitions are provided. Predicative adjectives are further distinguished into absolute and relative ones. The new concepts of set commensurability and rod commensurability are introduced too. 3. The existence of a plurality of social actors, with interest in the policy being assessed, causes that social decisions involve multiple types of values, of which economic efficiency is only one. Therefore it is misleading to make social decisions based only on that one value. 4. Weak comparability of values, which is grounded on incommensurability, is proved to be the main methodological foundation of policy evaluation in the framework of well-being economics. Incommensurability does not imply incomparability; on the contrary incommensurability is the only rational way to compare societal options under a plurality of policy objectives. 5. Weak comparability can be implemented by using multi-criteria evaluation, which is a formal framework for applied consequentialism under incommensurability. Social Multi-Criteria Evaluation, in particular, allows considering both technical and social incommensurabilities simultaneously.

Setting the rules of the game: The choice of electoral systems in advanced democracies

The origins of electoral systems have received scant attention in the literature. Looking at the history of electoral rules in the advanced world in the last century, this paper shows that the existing wide variation in electoral rules across nations can be traced to the strategic decisions that the current ruling parties, anticipating the coordinating consequences of different electoral regimes, make to maximize their representation according to the following conditions. On the one hand, as long as the electoral arena does not change substantially and the current electoral regime serves the ruling parties well, the latter have no incentives to modify the electoral regime. On the other hand, as soon as the electoral arena changes (due to the entry of new voters or a change in their preferences), the ruling parties will entertain changing the electoral system, depending on two main conditions: the emergence of new parties and the coordinating capacities of the old ruling parties. Accordingly, if the new parties are strong, the old parties shift from plurality/majority rules to proportional representation (PR) only if the latter are locked into a 'non-Duvergerian' equilibrium; i.e. if no old party enjoys a dominant position (the case of most small European states)--conversely, they do not if a Duvergerian equilibrium exists (the case of Great Britain). Similarly, whenever the new entrants are weak, a non-PR system is maintained, regardless of the structure of the old party system (the case of the USA). The paper discusses as well the role of trade and ethnic and religious heterogeneity in the adoption of PR rules.

Voting with preferences over margins of victory

This paper analyzes a two-alternative voting model with the distinctive feature that voters have preferences over margins of victory. We study voting contests with a finite as well as an infinite number of voters, and with and without mandatory voting. The main result of the paper is the existence and characterization of a unique equilibrium outcome in all those situations. At equilibrium, voters who prefer a larger support for one of the alternatives vote for such alternative.The model also provides a formal argument for the conditional sincerity voting condition in Alesina and Rosenthal (1995) and the benefit of voting function in Llavador (2006). Finally, we offer new insights on explaining why some citizens may vote strategically for an alternative different from the one declared as the most preferred.

On the origins of electoral systems and political parties. The role of elections in multi-member districts

The old, understudied electoral system composed of multi-member districts, open ballot and plurality rule is presented as the most remote scene of the origin of both political parties and new electoral systems. A survey of the uses of this set of electoral rules in different parts of the world during remote and recent periods shows its wide spread. A model of voting by this electoral system demonstrates that, while it can produce varied and pluralistic representation, it also provides incentives to form factional or partisan candidacies. Famous negative reactions to the emergence of factions and political parties during the 18th and 19th centuries are reinterpreted in this context. Many electoral rules and procedures invented since the second half of the 19th century, including the Australian ballot, single-member districts, limited and cumulative ballots, and proportional representation rules, derived from the search to reduce the effects of the originating multi-member district system in favor of a single party sweep. The general relations between political parties and electoral systems are restated to account for the foundational stage here discussed.

Negativity effect in multiparty electoral competition

We construct a dynamic voting model of multiparty competition in order to capture the following facts: voters base their decision on past economicperformance of the parties, and parties and candidates have different objectives. This model may explain the emergence of parties' ideologies,and shows the compatibility of the different objectives of parties and candidates. Together, these results give rise to the formation ofpolitical parties, as infinetely-lived agents with a certain ideology, out of the competition of myopic candidates freely choosing policy positions. We also show that in multicandidate elections held under the plurality system, Hotelling's principle of minimum differentiation is no longer satisfied.

On the justice of voting systems

What are the best voting systems in terms of utilitarianism? Or in terms of maximin, or maximax? We study these questions for the case of three alternatives and a class of structurally equivalent voting rules. We show that plurality, arguably the most widely used voting system, performs very poorly in terms of remarkable ideals of justice, such as utilitarianism or maximin, and yet is optimal in terms of maximax. Utilitarianism is bestapproached by a voting system converging to the Borda count, while the best way to achieve maximin is by means of a voting system converging to negative voting. We study the robustness of our results across different social cultures, measures of performance, and population sizes.

Contribución al diseño de GNSS-SDR, un receptor GNSS de código abierto

[ANGLÈS] This project introduces GNSS-SDR, an open source Global Navigation Satellite System software-defined receiver. The lack of reconfigurability of current commercial-of-the-shelf receivers and the advent of new radionavigation signals and systems make software receivers an appealing approach to design new architectures and signal processing algorithms. With the aim of exploring the full potential of this forthcoming scenario with a plurality of new signal structures and frequency bands available for positioning, this paper describes the software architecture design and provides details about its implementation, targeting a multiband, multisystem GNSS receiver. The result is a testbed for GNSS signal processing that allows any kind of customization, including interchangeability of signal sources, signal processing algorithms, interoperability with other systems, output formats, and the offering of interfaces to all the intermediate signals, parameters and variables. The source code release under the GNU General Public License (GPL) secures practical usability, inspection, and continuous improvement by the research community, allowing the discussion based on tangible code and the analysis of results obtained with real signals. The source code is complemented by a development ecosystem, consisting of a website (http://gnss-sdr.org), as well as a revision control system, instructions for users and developers, and communication tools. The project shows in detail the design of the initial blocks of the Signal Processing Plane of the receiver: signal conditioner, the acquisition block and the receiver channel, the project also extends the functionality of the acquisition and tracking modules of the GNSS-SDR receiver to track the new Galileo E1 signals available. Each section provides a theoretical analysis, implementation details of each block and subsequent testing to confirm the calculations with both synthetically generated signals and with real signals from satellites in space.

A comparison of mean phase difference and generalized least squares for analyzing single-case data

The present study focuses on single-case data analysis and specifically on two procedures for quantifying differences between baseline and treatment measurements The first technique tested is based on generalized least squares regression analysis and is compared to a proposed non-regression technique, which allows obtaining similar information. The comparison is carried out in the context of generated data representing a variety of patterns (i.e., independent measurements, different serial dependence underlying processes, constant or phase-specific autocorrelation and data variability, different types of trend, and slope and level change). The results suggest that the two techniques perform adequately for a wide range of conditions and researchers can use both of them with certain guarantees. The regression-based procedure offers more efficient estimates, whereas the proposed non-regression procedure is more sensitive to intervention effects. Considering current and previous findings, some tentative recommendations are offered to applied researchers in order to help choosing among the plurality of single-case data analysis techniques.

Boris Vian dans ses poèmes

El artículo se propone mostrar cómo el estudio de los poemas y canciones de Boris Vian sólo cobra sentido mediante un análisis de conjunto. Tras la aparente dispersión de temas y estilos, bajo la apariencia superficial, cómica y en ocasiones incluso grotesca y banal de sus poemas y canciones, se oculta una unidad y una coherencia profundas y minuciosamente calculadas. Para expresarla Vian huye de las limitaciones de la lógica heredada de Aristóteles y opta por utilizar la técnica del collage, yuxtaponiendo una pluralidad de situaciones y acciones en las que lo real se entremezcla con lo imaginario, cuyo resultado final es la representación de una realidad única, indivisible y a la vez relativa y singular en función de cada individuo, en la que los aparentes antagonismos se revelan como elementos complementarios en el proceso de individualización y conocimiento del «yo» interior.

Conocimiento del catalán y castellano por parte del alumnado inmigrante

A lo largo de la última década en Cataluña, la heterogeneidad identitaria, lingüística, cultural y étnica ha crecido de manera importante. En consecuencia, nuestras escuelas se han transformado en centros donde la pluralidad étnica, religiosa, cultural y lingüística es cada día más evidente. Pero, a diferencia de otros territorios del Estado, una de las características fundamentales de nuestro Sistema Educativo es su organización bajo los parámetros de la educación bilingüe. De esta manera, además de un profundo dominio del catalán, lengua propia de Cataluña y lengua usada como vehicular y de aprendizaje en la enseñanza, se persigue un buen conocimiento de la lengua castellana. En este contexto, diferentes estudios ponen en evidencia el papel clave del dominio de la lengua de la escuela tanto de cara a garantizar el éxito escolar como para la integración y la cohesión social. Con este marco de fondo, nos situamos en el caso del Instituto de Educación Secundaria (IES) de Guissona, en la comarca de la Segarra, donde por circunstancias diversas el fenómeno migratorio ha sido muy importante a lo largo de la última década. El objetivo de nuestra investigación es el análisis de las competencias lingüísticas del alumnado de dicho centro, tomando como referencia el nivel de competencia lingüística de sus iguales autóctonos.En concreto, a partir de una muestra de 28 niños y niñas inmigrantes que fueron comparados con un grupo de 93 escolares autóctonos de su misma edad y nivel escolar, nuestro trabajo analiza el desarrollo de diferentes habilidades en lengua catalana y castellana.

Escriure (a) la frontera : autores bilingües traductores culturals

La creixent literatura postcolonial en països prèviament colonitzats, així com la creixent literatura de minories en països primermundistes sovint posen de manifest un mestissatge cultural que queda palès en la llengua. Les escriptores bilingües d’aquests països ocupen un espai cultural fronterer, com a mínim, a cavall de dos mons, a cavall de dues identitats i a cavall de dues llengües. La seva lectura del món no tan sols posa de manifest la problemàtica de la pluralitat lingüística i la diversitat d’identitats en les persones humanes, sinó que també acara l’essencialisme de les nocions d’equivalència que les expressions culturals dominants han presentat al llarg de la història de la traducció.

Institutional Determinants of Military Spending

Drawing on a database for 1988-2006 containing information on 157 countries, we investigate the effects on military spending of government form, electoral rules, concentration of parliamentary parties, and ideology. From an OLS regression on pooled data, our results show that presidential democracies spend more than parliamentary systems on defense, whereas the presence of a plurality voting system will reduce the defense burden. Our findings suggest that, in contrast to theoretical predictions in the literature, institutions do not have the same impact on the provision of all public goods. We present as well evidence regarding the effect of ideology on defense spending.