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.

The Criminal Justice Approach : Case Exemples

This article provides an overview of the various forms of proceedings available within 11 European criminal justice systems and reflects upon their core features. It also provides a picture of how far alternative, non-criminal proceedings are used by some of the systems as a different path to imposing a state reaction upon wrong-doers.

La nueva política criminal de la seguridad vial. Reflexiones a propósito de la LO 15/2007, de 30 de noviembre, y del Proyecto de Reforma del Código Penal

La reforma de los delitos contra la seguridad en el tráfico operada por LO 15/2007, de 30 de noviembre, constituye la expresión de un programa político-criminal de más amplio alcance, presente en el Proyecto de Reforma del Código Penal de 2007. En este trabajo se exponen las causas de la emergencia del nuevo derecho penal de la seguridad vial a la luz del paradi gma explicativo que ofrece el derecho penal postmoderno del riesgo -sometido aquí a necesarios ajustes- y se ofrece un análisis crítico de dos de los nuevos tipos: la conducción a velocidad por encima de determinados límites (art. 379.1) y la conducción con concentraciones de alcohol en aire espirado o en sangre superiores a determinadas tasas (0.6 mgr. o 1,2 gr. respectivamente) –art. 379.2-. Igualmente se analiza la propuesta del Proyecto de Reforma del Código de elevar a la categoría de delito las imprudencias leves con resultado de muerte. Tres piezas clave de un programa que trasluce una gran desconfianza hacia el estamento judicial y un optimismo infundado en las posibilidades del derecho penal para reducir eficazmente la siniestralidad vial.

Sistema de sanciones y política criminal: un estudio de Derecho comparado europeo

El trabajo aborda una comparación de los diversos sistemas de penas estatales en Europa, con el objetivo de sistematizar los diversos modelos político-criminales y de calibrar la aflictividad de los mismos. A través de determinados indicadores se pone de relieve que los sistemas jurídicos que abren un mayor espacio a la discrecionalidad judicial en la selección y la determinación de la pena muestran una mayor moderación del rigor punitivo y están en mejores condiciones de dar respuesta a una fenomenología criminal cada vez más diversa.

Política criminal con bases empíricas en España

La dimensión real de la actual política criminal española carece de adecuados niveles de racionalidad, entre sus múltiples causas, podemos mencionar el fenómeno de la creciente dinámica punitivista, la ausencia de una adecuada cultura de evaluación, el menosprecio a la criminología, la escasa consideración de los responsables políticos hacia las opiniones expertas de la dogmática, y la constante indiferencia de ésta hacia la realidad que debe enfrentar. Se configura así un decepcionante panorama donde la política criminal real aparece como carente de una sólida base empírica. La dimensión teórica de la política criminal, no puede soslayar el aporte de las investigaciones criminológicas, ya que aquellos tendrían la virtualidad de ser condición necesaria aunque no suficiente de la utilización racional del sistema punitivo. Hay que optar por una reducción de la privación de libertad y promover otras sanciones en cuyo contenido se armonicen los conceptos de incapacitación y responsabilización. Además, se requiere el desarrollo de una victimología que se dirija a inhibir los impulsos punitivos de las víctimas en función de orientar la política criminal hacia una cultura jurídica reparatoria que enfrente la actual expansión del derecho penal.

Food traditions and landscape histories of the Indian Ocean World : theoretical and methodological reflections

Environmental histories of plant exchanges have largely centred on their eco- nomic importance in international trade and on their ecological and social impacts in the places where they were introduced. Yet few studies have at- tempted to examine how plants brought from elsewhere become incorporated over time into the regional cultures of material life and agricultural landscapes. This essay considers the theoretical and methodological problems in inves- tigating the environmental history, diversity and distribution of food plants transferred across the Indian Ocean over several millennia. It brings together concepts of creolisation, syncretism, and hybridity to outline a framework for understanding how biotic exchanges and diffusions have been translated into regional landscape histories through food traditions, ritual practices and articu- lation of cultural identity. We use the banana plant - which underwent early domestication across New Guinea, South-east Asia and peninsular India and reached East Africa roughly two thousand years ago - as an example for il- lustrating the diverse patterns of incorporation into the cultural symbolism, material life and regional landscapes of the Indian Ocean World. We show that this cultural evolutionary approach allows new historical insights to emerge and enriches ongoing debates regarding the antiquity of the plant's diffusion from South-east Asia to Africa.

Current Sheet Regulation of Solar Near-relativistic Electron Injection Histories

We present a sample of three large near-relativistic (>50 keV) electron events observed in 2001 by both the ACE and the Ulysses spacecraft, when Ulysses was at high-northern latitudes (>60◦) and close to 2 AU. Despite the large latitudinal distance between the two spacecraft, electrons injected near the Sun reached both heliospheric locations. All three events were associated with large solar flares, strong decametric type II radio bursts and accompanied by wide (>212◦) and fast (>1400 km s−1) coronal mass ejections (CMEs). We use advanced interplanetary transport simulations and make use of the directional intensities observed in situ by the spacecraft to infer the electron injection profile close to the Sun and the interplanetary transport conditions at both low and high latitudes. For the three selected events, we find similar interplanetary transport conditions at different heliolatitudes for a given event, with values of the mean free path ranging from 0.04 AU to 0.27 AU. We find differences in the injection profiles inferred for each spacecraft. We investigate the role that sector boundaries of the heliospheric current sheet (HCS) have on determining the characteristics of the electron injection profiles. Extended injection profiles, associated with coronal shocks, are found if the magnetic footpoints of the spacecraft lay in the same magnetic sector as the associated flare, while intermittent sparse injection episodes appear when the spacecraft footpoints are in the opposite sector or a wrap in the HCS bounded the CME structure.

Tracking Invasion Histories in the Sea: Facing Complex Scenarios Using Multilocus Data

In recent years, new analytical tools have allowed researchers to extract historical information contained in molecular data, which has fundamentally transformed our understanding of processes ruling biological invasions. However, the use of these new analytical tools has been largely restricted to studies of terrestrial organisms despite the growing recognition that the sea contains ecosystems that are amongst the most heavily affected by biological invasions, and that marine invasion histories are often remarkably complex. Here, we studied the routes of invasion and colonisation histories of an invasive marine invertebrate Microcosmus squamiger (Ascidiacea) using microsatellite loci, mitochondrial DNA sequence data and 11 worldwide populations. Discriminant analysis of principal components, clustering methods and approximate Bayesian computation (ABC) methods showed that the most likely source of the introduced populations was a single admixture event that involved populations from two genetically differentiated ancestral regions - the western and eastern coasts of Australia. The ABC analyses revealed that colonisation of the introduced range of M. squamiger consisted of a series of non-independent introductions along the coastlines of Africa, North America and Europe. Furthermore, we inferred that the sequence of colonisation across continents was in line with historical taxonomic records - first the Mediterranean Sea and South Africa from an unsampled ancestral population, followed by sequential introductions in California and, more recently, the NE Atlantic Ocean. We revealed the most likely invasion history for world populations of M. squamiger, which is broadly characterized by the presence of multiple ancestral sources and non-independent introductions within the introduced range. The results presented here illustrate the complexity of marine invasion routes and identify a cause-effect relationship between human-mediated transport and the success of widespread marine non-indigenous species, which benefit from stepping-stone invasions and admixture processes involving different sources for the spread and expansion of their range.

Current Sheet Regulation of Solar Near-Relativistic Electron Injection Histories

We present a sample of three large near-relativistic (>50 keV) electron events observed in 2001 by both the ACE and the Ulysses spacecraft, when Ulysses was at high-northern latitudes (>60°) and close to 2 AU. Despite the large latitudinal distance between the two spacecraft, electrons injected near the Sun reached both heliospheric locations. All three events were associated with large solar flares, strong decametric type II radio bursts and accompanied by wide (>212°) and fast (>1400 km s-1) coronal mass ejections (CMEs). We use advanced interplanetary transport simulations and make use of the directional intensities observed in situ by the spacecraft to infer the electron injection profile close to the Sun and the interplanetary transport conditions at both low and high latitudes. For the three selected events, we find similar interplanetary transport conditions at different heliolatitudes for a given event, with values of the mean free path ranging from 0.04 AU to 0.27 AU. We find differences in the injection profiles inferred for each spacecraft. We investigate the role that sector boundaries of the heliospheric current sheet (HCS) have on determining the characteristics of the electron injection profiles. Extended injection profiles, associated with coronal shocks, are found if the magnetic footpoints of the spacecraft lay in the same magnetic sector as the associated flare, while intermittent sparse injection episodes appear when the spacecraft footpoints are in the opposite sector or a wrap in the HCS bounded the CME structure.

To analyse a trace or not? Evaluating the decision-making process in the criminal investigation

In order to broaden our knowledge and understanding of the decision steps in the criminal investigation process, we started by evaluating the decision to analyse a trace and the factors involved in this decision step. This decision step is embedded in the complete criminal investigation process, involving multiple decision and triaging steps. Considering robbery cases occurring in a geographic region during a 2-year-period, we have studied the factors influencing the decision to submit biological traces, directly sampled on the scene of the robbery or on collected objects, for analysis. The factors were categorised into five knowledge dimensions: strategic, immediate, physical, criminal and utility and decision tree analysis was carried out. Factors in each category played a role in the decision to analyse a biological trace. Interestingly, factors involving information available prior to the analysis are of importance, such as the fact that a positive result (a profile suitable for comparison) is already available in the case, or that a suspect has been identified through traditional police work before analysis. One factor that was taken into account, but was not significant, is the matrix of the trace. Hence, the decision to analyse a trace is not influenced by this variable. The decision to analyse a trace first is very complex and many of the tested variables were taken into account. The decisions are often made on a case-by-case basis.

La reforma de la Ley de Enjuiciamiento Criminal

El present treball pretén oferir al lector un estudi sobre el nou Codi Processal Penal com esborrany d'avantprojecte de Llei, realitzant un anàlisis dels aspectes més rellevants i innovadors que introdueix el citat Codi així com l’adaptació d’aquests a les realitats socials de cada temps. A més, la idea per la qual neix el treball és analitzar les raons per les quals s’ha vist necessari i important realitzar una modificació total de la actual LECrim, estudiant la forma en què el legislador enfoca el nou Codi així com el seu contingut, destacant les principals diferències que conté l’actual LECrim amb aquelles que el nou Codi pretén instaurar.

Patrícia Melo. Novela de favela y novela criminal. Género(s)

El artículo se propone reflexionar sobre dos cuestiones: ¿la «novela de favela» es novela criminal? y ¿es posible detectar aspectos de género en las «novelas de favela» de Patrícia Melo? En nuestra opinión, la «novela de favela» es literatura de la violencia, para ser más exactos de la representación de la violencia, pero, aunque a veces la frontera sea muy tenue, no responde a los paradigmas de la novela criminal. Por otra parte, y a partir del análisis de la construcción de los personajes Máiquel y Reizinho (O Matador e Inferno), creemos que sí es posible afirmar un sesgo de género en los textos de Patrícia Melo.

Strategic practices : : hidden histories of gender in Finland 1880-2005 : projektikuvaus

Ajankohtaista

A myriad of small histories and personal experiences

Kirjallisuusarvostelu