Molecular analysis of evolutionary relationships of Phaseolus dumosus with the gene pool of common bean

Valuable genetic variation for bean breeding programs is held within the common bean secondary gene pool which consists of Phaseolus albescens, P. coccineus, P. costaricensis, and P. dumosus. However, the use of close relatives for bean improvement is limited due to the lack of knowledge about genetic variation and genetic plasticity of many of these species. Characterisation and analysis of the genetic diversity is necessary among beans' wild relatives; in addition, conflicting phylogenies and relationships need to be understood and a hypothesis of a hybrid origin of P. dumosus needs to be tested. This thesis research was orientated to generate information about the patterns of relationships among the common bean secondary gene pool, with particular focus on the species Phaseolus dumosus. This species displays a set of characteristics of agronomic interest, not only for the direct improvement of common bean but also as a source of valuable genes for adaptation to climate change. Here I undertake the first comprehensive study of the genetic diversity of P. dumosus as ascertained from both nuclear and chloroplast genome markers. A germplasm collection of the ancestral forms of P. dumosus together with wild, landrace and cultivar representatives of all other species of the common bean secondary gene pool, were used to analyse genetic diversity, phylogenetic relationships and structure of P. dumosus. Data on molecular variation was generated from sequences of cpDNA loci accD-psaI spacer, trnT-trnL spacer, trnL intron and rps14-psaB spacer and from the nrDNA the ITS region. A whole genome DArT array was developed and used for the genotyping of P. dumosus and its closes relatives. 4208 polymorphic markers were generated in the DArT array and from those, 742 markers presented a call rate >95% and zero discordance. DArT markers revealed a moderate genetic polymorphism among P. dumosus samples (13% of polymorphic loci), while P. coccineus presented the highest level of polymorphism (88% of polymorphic loci). At the cpDNA one ancestral haplotype was detected among all samples of all species in the secondary genepool. The ITS region of P. dumosus revealed high homogeneity and polymorphism bias to P. coccineus genome. Phylogenetic reconstructions made with Maximum likelihood and Bayesian methods confirmed previously reported discrepancies among the nuclear and chloroplast genomes of P. dumosus. The outline of relationships by hybridization networks displayed a considerable number of interactions within and between species. This research provides compelling evidence that P. dumosus arose from hybridisation between P. vulgaris and P. coccineus and confirms that P. costaricensis has likely been involved in the genesis or backcrossing events (or both) in the history of P. dumosus. The classification of the specie P. persistentus was analysed based on cpDNA and ITS sequences, the results found this species to be highly related to P. vulgaris but not too similar to P. leptostachyus as previously proposed. This research demonstrates that wild types of the secondary genepool carry a significant genetic variation which makes this a valuable genetic resource for common bean improvement. The DArT array generated in this research is a valuable resource for breeding programs since it has the potential to be used in several approaches including genotyping, discovery of novel traits, mapping and marker-trait associations. Efforts should be made to search for potential populations of P. persistentus and to increase the collection of new populations of P. dumosus, P. albescens and P. costaricensis that may provide valuable traits for introgression into common bean and other Phaseolus crops.

Terrigenous input and marine productivity for the Pacific sector of the Southern Ocean based on lipid biomarkers

In this study, we present a new multiproxy data set of terrigenous input, marine productivity and sea surface temperature (SST) from 52 surface sediment samples collected along E-W transects in the Pacific sector of the Southern Ocean. Allochtonous terrigenous input was characterized by the distribution of plant wax n-alkanes and soil-derived branched glycerol dialkyl glycerol tetraethers (brGDGTs). 230Th-normalized burial rates of both compound groups were highest close to the potential sources in Australia and New Zealand and are strongly related to lithogenic contents, indicating common sources and transport. Detection of both long-chain n-alkanes and brGDGTs at the most remote sites in the open ocean strongly suggests a primarily eolian transport mechanism to at least 110°W, i.e. by prevailing westerly winds. Two independent organic SST proxies were used, the UK'37 based on long-chain alkenones, and the TEX86 based on isoprenoid GDGTs. Both, UK'37 and TEX86 indices show robust relationships with temperature over a temperature range between 0.5 and 20°C, likely implying different seasonal and regional imprints on the temperature signal. While alkenone-based temperature estimates reliably reflect modern SST even at the low temperature end, large temperature residuals are observed for the polar ocean using the TEX86 index. 230Th-normalized burial rates of alkenones are highest close to the Subtropical Front and are positively related to lithogenic fluxes throughout the study area. In contrast, highest isoGDGT burial south of the Antarctic Polar Front is not related with dust flux but may be largely controlled by diatom blooms, and thus high opal fluxes during austral summer.

Boron isotope and B/Ca ratios of planktonic foraminifera

Here a new analytical methodology is described for measuring the isotopic composition of boron in foraminifera using multicollector inductively coupled plasma mass spectrometry (MC-ICPMS). This new approach is fast (~10 samples analysed in duplicate per analytical session) and accurate (to better than 0.25 per mil at 95% confidence) with acceptable sample size requirements (1-3 mg of carbonate). A core top calibration of several common planktic and two benthic species from geographically widespread localities shows a very close agreement between the isotopic composition measured by MC-ICPMS and the isotopic composition of B(OH)-4 in seawater (as predicted using the recently measured isotopic equilibrium factor of 1.0272) at the depth of habitat. A down core and core top investigation of boron concentration (B/Ca ratio) shows that the partition coefficient is influenced by [CO2-3] complicating the application of this proxy. Nevertheless, it is demonstrated that these two proxies can be used to fully constrain the carbonate system of surface water in the Caribbean Sea (ODP Site 999A) over the last 130 kyr. This reconstruction shows that during much of the Holocene and the last interglacial period surface water at Site 999A was in equilibrium with the atmosphere with respect to CO2. During the intervening colder periods although the surface water pCO2 was lower than the Holocene, it was a minor to significant source of CO2 to the atmosphere possibly due to either an expansion of the eastern equatorial Atlantic upwelling zone, or a more local expansion of coastal upwelling in the southern Caribbean. Such reorganisation of the oceanic carbonate system in favour of a larger source of CO2 to the atmosphere from the equatorial ocean may require mechanisms responsible for lowering atmospheric CO2 during glacial periods to be more efficient than previously supposed.

The Comparative Effectiveness of EEG Biomarkers in Antidepressant Response and Illness Prediction in Major Depressive Disorder

Background: There is growing evidence that individual EEG differences may aid in classifying patients with major depressive disorder (MDD) and also help predict clinical response to antidepressant treatment. This study aims to compare the effectiveness of EEG frequency band power, alpha asymmetry and prefrontal theta cordance towards escitalopram response prediction and MDD diagnosis, in a multi-site initiative. Methods: Resting EEG (eyes open and closed) was recorded from 64 electrodes in 44 depressed patients and 20 healthy controls at baseline, 2 weeks post-treatment and 8 weeks post-treatment. Clinical response was measured as change from baseline MADRS of 50% or more. EEG measures were analyzed (1) at baseline (2) at 2 weeks post-treatment and (3) as an ‘‘early change” variable defined as change in EEG from baseline to 2 weeks post-treatment. Results: At baseline, responders exhibited greater absolute alpha power in the left hemisphere versus the right while non-responders showed the opposite. Responders further exhibited a cortical asymmetry of greater right relative to left activity in parietal areas. Groups also differed in baseline relative delta power with responders showing greater power in the right hemisphere versus the left while non-responders showed the opposite. At 2 weeks post-treatment, responders exhibited greater absolute beta power in the left hemisphere relative to right and the opposite was noted for non-responders. The opposite pattern was noted for absolute and relative delta power at 2 weeks post-treatment. Responders exhibited early reduction in relative alpha power and early increments in relative theta power. Non-responders showed a significant early increase in prefrontal theta cordance. Absolute delta power helped distinguish MDD patients from healthy controls. Conclusions: Hemispheric asymmetries in the alpha and delta bands at pre-treatment baseline and at 2 weeks post-treatment have moderate to moderately strong predictive utility towards antidepressant treatment response. These findings have significant potential for improving clinical practice in psychiatry by eventually guiding clinical choice of treatments. This would greatly benefit patients awaiting relief from depressive symptoms as treatment optimization would help overcome problems associated with delayed recovery. Our results also indicate that resting EEG activity may have clinical utility in predicting MDD diagnosis.

Bipartite Assertion: A New Account of Assertion, Defined in Terms of Responsibility and Explicit Presentation

Assertion is a speech act that stands at the intersection of the philosophy of language and social epistemology. It is a phenomenon that bears on such wide-ranging topics as testimony, truth, meaning, knowledge and trust. It is thus no surprise that analytic philosophers have devoted innumerable pages to assertion, trying to give the norms that govern it, its role in the transmission of knowledge, and most importantly, what assertion is, or how assertion is to be defined. In this thesis I attempt to show that all previous answers to the question “What is assertion?” are flawed. There are four major traditions in the literature: constitutive norm theories of assertion, accounts that treat assertion as the expression of speaker attitudes, accounts that treat assertion as a proposal to add some proposition to the common ground, and accounts that treat assertion as the taking of responsibility for some claim. Each tradition is explored here, the leading theories within the tradition developed, and then placed under scrutiny to demonstrate flaws within the positions surveyed. I follow the work of G.E. Moore and William P. Alston, whilst drawing on the work of Robert Brandom in order to give a new bipartite theory of assertion. I argue that assertion consists in the explicit presentation of a proposition, along with a taking of responsibility for that proposition. Taking Alston's explicit presentation condition and repairing it in order to deal with problems it faces, whilst combining it with Brandom's responsibility condition, provides, I believe, the best account of assertion.

Fossil associations from the middle and upper Eocene strata of the Pamplona Basin and surrounding areas (Navarre, western Pyrenees)

Fossil associations from the middle and upper Eocene (Bartonian and Priabonian) sedimentary succession of the Pamplona Basin are described. This succession was accumulated in the western part of the South Pyrenean peripheral foreland basin and extends from deep-marine turbiditic (Ezkaba Sandstone Formation) to deltaic (Pamplona Marl, Ardanatz Sandstone and Ilundain Marl formations) and marginal marine deposits (Gendulain Formation). The micropalaeontological content is high. It is dominated by foraminifera, and common ostracods and other microfossils are also present. The fossil ichnoasssemblages include at least 23 ichnogenera and 28 ichnospecies indicative of Nereites, Cruziana, Glossifungites and ?Scoyenia-Mermia ichnofacies. Body macrofossils of 78 taxa corresponding to macroforaminifera, sponges, corals, bryozoans, brachiopods, annelids, molluscs, arthropods, echinoderms and vertebrates have been identified. Both the number of ichnotaxa and of species (e. g. bryozoans, molluscs and condrichthyans) may be considerably higher. Body fossil assemblages are comparable to those from the Eocene of the Nord Pyrenean area (Basque Coast), and also to those from the Eocene of the west-central and eastern part of South Pyrenean area (Aragon and Catalonia). At the European scale, the molluscs assemblages seem endemic from the Pyrenean area, although several Tethyan (Italy and Alps) and Northern elements (Paris basin and Normandy) have been recorded. Palaeontological data of studied sedimentary units fit well with the shallowing process that throughout the middle and late Eocene occurs in the area, according to the sedimentological and stratigraphical data.

The State of the Nation Debate as part of the democratic parliamentary ritual: Rajoy and Rubalcaba discourse analysis, 2014

In this article we analyze the Debate on the State of the Nation 2014. The methodology consists in coding the speeches of the prime minister, Mariano Rajoy (PP) and the then opposition leader Alfredo Perez Rubalcaba (PSOE) through extracting word clouds, branched maps and word trees that have shown the most common concepts and premises. This preliminary analysis of two dimensions, quantitative and qualitative, makes it much easier and viable subsequent discourse analysis where we focus on the different types of arguments in the communicative act: claim/solution, circumstantial premises, goal premises, value premises, meansgoal premises, alternative options/addressing alternative options.

The influence of balanced and imbalanced resource supply on biodiversity – functioning relationship across ecosystems

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

The influence of balanced and imbalanced resource supply on biodiversity – functioning relationship across ecosystems

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

Multilingualism and conceptual modelling

One of the leading motivations behind the multilingual semantic web is to make resources accessible digitally in an online global multilingual context. Consequently, it is fundamental for knowledge bases to find a way to manage multilingualism and thus be equipped with those procedures for its conceptual modelling. In this context, the goal of this paper is to discuss how common-sense knowledge and cultural knowledge are modelled in a multilingual framework. More particularly, multilingualism and conceptual modelling are dealt with from the perspective of FunGramKB, a lexico-conceptual knowledge base for natural language understanding. This project argues for a clear division between the lexical and the conceptual dimensions of knowledge. Moreover, the conceptual layer is organized into three modules, which result from a strong commitment towards capturing semantic knowledge (Ontology), procedural knowledge (Cognicon) and episodic knowledge (Onomasticon). Cultural mismatches are discussed and formally represented at the three conceptual levels of FunGramKB.

Law and Original Contract in the Republican Thought of Immanuel Kant

This article discusses the concept of right and its identification with the power to coerce, to show a reciprocity between the original contract and the right, as a manifestation of the reciprocity between moral law and freedom, as Kant states in its Second Critique. The demonstration of this view will allow a republican stance evident in the legal and political thought of Kant, since the right of a people can only exist while the town itself is unified to enact.

The Challenge of Migration and the Global Security Strategy of the European Union

This article discusses the challenges of irregular migration for the security of the EU. They are analyzed starting with the European Security Strategy 2003, and the Report on its Implementation, 2008, and notes many failures: The EU Members did not follow the directives adopted in Brussels, the mismanagement of migration and asylum policies, and numerous actions that can be characterized or described as improvised, scattered or irresponsible. The 2016 Global Strategy recognizes these failures and call attention to the European leaders to reconsider how the EU functions and operates, suggesting the need for greater unity and cooperation to achieve a more effective migration policy. However, the article points out that practically all of the sections of the new Strategy dealing with migration were already embodied in previous Strategies, and stress that in parallel with the publication of the 2016 Global Strategy, actions are already undertaken, such as the EU readmission agreements signed with several important third countries of origin.

Commentary on Maugham's Treatise on the Laws of Literary Property (1828)

The first British legal treatise dedicated specifically to the law of copyright written by a strong advocate of the common law rights of the author. Maugham, in addition to providing a commentary upon the law of copyright, also used his work to lobby for both an extension to the copyright term (ideally resulting in a perpetual right) and a reduction in the library deposit requirements (arguing that authors should only be required to deposit one copy of their work for the British Museum). In proselytising the need for a change to the law in both areas he drew frequent comparisons with the law of other jurisdictions (in particular France and Germany). The work became a standard point of reference for many British and American authors who followed.

The effectiveness of community-based interventions to improve maternal and infant health in the Northeast of Brazil

EMOND, Alan et al. The effectiveness of community-based interventions to improve maternal and infant health in the Northeast of Brazil. Revista Panamericana de Salud Pública/ Pan American Journal of Public Health , v.12, n.2, p.101-110, 2002

Justice envers les enfants et légitimité politique en éducation

L’idée selon laquelle les enfants sont des sujets à part entière de considérations de justice n’est pas très contestée. Les enfants ont des intérêts qui leur sont propres et ont un statut moral indépendant de leurs parents : ils ne sont ni la propriété de ces derniers ni une simple extension de leur personne. Pourtant, les travaux des plus grands théoriciens de la justice en philosophie politique contemporaine ne contiennent pas de discussion systématique du statut moral et politique des enfants et du contenu de nos obligations à leur égard. Cette thèse contribue à remédier à cette omission à travers l’examen de quatre grandes questions principales. (1) Quelles sont les obligations de justice de l’état libéral envers les enfants ? (2) Quels types de politiques publiques en matière d’éducation des enfants sont moralement légitimes ? (3) Jusqu’à quel point est-il moralement acceptable pour les parents de délibérément forger la vision du monde de leurs enfants ? (4) Quels critères moraux devraient guider l’élaboration de politiques en matière d’éducation morale dans les écoles ? Cette thèse est constituée de quatre articles. Le premier, « Political Liberalism and Children’s Education », aborde les questions du fondement normatif et des implications du principe de ‘neutralité éducative’ ou ‘anti-perfectionnisme éducatif’. Selon ce principe, il n’est pas légitime pour l’État libéral de délibérément promouvoir, à travers ses politiques publiques en éducation, une conception particulière de la vie bonne. L’article défend les idées suivantes. D’abord, ledit principe est exclusivement fondé sur des raisons de justice envers les parents. Ensuite, l’anti-perfectionnisme libéral n’est pas, pour autant, ‘mauvais pour les enfants’, puisqu’une vaste gamme d’interventions politiques dans la vie familiale et l’éducation des enfants sont, de manière surprenante, justifiables dans ce cadre théorique. Le deuxième article, « On the Permissibility of Shaping Children’s Values », examine la question de savoir si les parents ont un droit moral de forger délibérément l’identité, la conception du monde et les valeurs de leurs enfants. L’article développe une critique de la conception anti-perfectionniste des devoirs parentaux et propose un nouvel argument libéral à l’appui d’un droit parental conditionnel de forger l’identité de leurs enfants. L’article introduit également une distinction importante entre les notions d’éducation compréhensive et d’« enrôlement » compréhensif. Le troisième article, « Common Education and the Practice of Liberal Neutrality: The Loyola High School Case », défend trois thèses principales à travers une analyse normative de l’affaire juridique de l’école Loyola. Premièrement, il est légitime pour l’État libéral d’adopter un modèle d’éducation commune fort. Deuxièmement, la thèse selon laquelle la neutralité comme approche éducative serait impossible est injustifiée. Troisièmement, il existe néanmoins de bonnes raisons pour l’État libéral d’accommoder plusieurs écoles religieuses qui rejettent le modèle de la neutralité. Le quatrième article, « Which Moral Issues Should be Taught as Controversial? », critique à la fois le critère ‘épistémique’ dominant pour déterminer quels enjeux moraux devraient être enseignés aux jeunes comme ‘controversés’, et à la fois la manière dont le débat sur l’enseignement des enjeux controversés fut construit au cours des dernières années, d’un point de vue substantiel et méthodologique. L’article propose une manière alternative d’aborder le débat, laquelle prend adéquatement en compte la pluralité des objectifs de l’éducation et un ensemble d’autres considérations morales pertinentes.