Modeling magnetar outbursts: flux enhancements and the connection with short bursts and glitches

The availability of a large amount of observational data recently collected from magnetar outbursts is now calling for a complete theoretical study of outburst characteristics. In this Letter (the first of a series dedicated to modeling magnetar outbursts), we tackle the long-standing open issue of whether or not short bursts and glitches are always connected to long-term radiative outbursts. We show that the recent detection of short bursts and glitches seemingly unconnected to outbursts is only misleading our understanding of these events. We show that, in the framework of the starquake model, neutrino emission processes in the magnetar crust limit the temperature, and therefore the luminosity. This natural limit to the maximum luminosity makes outbursts associated with bright persistent magnetars barely detectable. These events are simply seen as a small luminosity increase over the already bright quiescent state, followed by a fast return to quiescence. In particular, this is the case for 1RXS J1708–4009, 1E 1841–045, SGR 1806–20, and other bright persistent magnetars. On the other hand, a similar event (with the same energetics) in a fainter source will drive a more extreme luminosity variation and longer cooling time, as for sources such as XTE J1810–197, 1E 1547–5408, and SGR 1627–41. We conclude that the non-detection of large radiative outbursts in connection with glitches and bursts from bright persistent magnetars is not surprising per se, nor does it need any revision of the glitches and burst mechanisms as explained by current theoretical models.

First molar size and wear within and among modern hunter-gatherers and agricultural populations

Apart from reflecting modern human dental variation, differences in dental size among populations provide a means for studying continuous evolutionary processes and their mechanisms. Dental wear, on the other hand, has been widely used to infer dietary adaptations and variability among or within diverse ancient human populations. Few such studies have focused on modern foragers and farmers, however, and diverse methods have been used. This research aimed to apply a single, standardized, and systematic quantitative procedure to measure dental size and dentin exposure in order to analyze differences among several hunter-gatherer and agricultural populations from various environments and geographic origins. In particular, we focused on sexual dimorphism and intergroup differences in the upper and lower first molars. Results indicated no sexual dimorphism in molar size and wear within the studied populations. Despite the great ethnographic variation in subsistence strategies among these populations, our findings suggest that differences in sexual division of labor do not affect dietary wear patterns.

The white gene and locomotor recovery from anoxia in Drosophila melanogaster

Locomotor recovery from anoxia is complicated and little is known about the molecular and cellular mechanisms regulating anoxic recovery in Drosophila. For this thesis I established a protocol for large-scale analysis of locomotor activity in adult flies with exposure to a transient anoxia. Using this protocol I observed that wild-type Canton-S flies recovered faster and more consistently from anoxia than the white-eyed mutant w1118, which carries a null allele of w1118 in an isogenic genetic background. Both Canton-S and w1118 are commonly used controls in the Drosophila community. Genetic analysis including serial backcrossing, RNAi knockdown, w+ duplication to Y chromosome as well as gene mutation revealed a strong association between the white gene and the timing of locomotor recovery. I also found that the locomotor recovery phenotype is independent of white-associated eye pigmentation, that heterozygous w+ allele was haplo-insufficient to induce fast and consistent locomotor recovery from anoxia in female flies, and that mini-white is insufficient to promote fast and consistent locomotor recovery. Moreover, locomotor recovery was delayed in flies with RNAi knockdown of white in subsets of serotonin neurons in the central nervous system. I further demonstrated that mutations of phosphodiesterase genes (PDE) displayed wild-type-like fast and consistent locomotor recovery, and that locomotor recovery was light-sensitive in the night in w1118. The delayed locomotor recovery and the light sensitivity were eliminated in PDE mutants that were dual-specific or cyclic guanosine monophosphate (cGMP)-specific. Up-regulation of cGMP using multiple approaches including PDE mutation, sildenafil feeding or specific expression of an atypical soluble guanylyl cyclase (Gyc88E) was sufficient to suppress w-RNAi induced delay of locomotor recovery. Taken together, these data strongly support the hypothesis that White transports cGMP and promotes fast and consistent locomotor recovery from anoxia.

Europe’s most wanted? Recalibrating Trust in the European Arrest Warrant System. CEPS Paper Liberty and Security in Europe 55/21 March 2013

This paper assesses the uses and misuses in the application of the European Arrest Warrant (EAW) system in the European Union. It examines the main quantitative results of this extradition system achieved between 2005 and 2011 on the basis of the existing statistical knowledge on its implementation at EU official levels. The EAW has been anchored in a high level of ‘mutual trust’ between the participating states’ criminal justice regimes and authorities. This reciprocal confidence, however, has been subject to an increasing number of challenges resulting from its practical application, presenting a dual conundrum: 1. Principle of proportionality: Who are the competent judicial authorities cooperating with each other and ensuring that there are sufficient impartial controls over the necessity and proportionality of the decisions on the issuing and execution of EAWs? 2. Principle of division of powers: How can criminal justice authorities be expected to handle different criminal judicial traditions in what is supposed to constitute a ‘serious’ or ‘minor’ crime in their respective legal settings and ‘who’ is ultimately to determine (divorced from political considerations) when is it duly justified to make the EAW system operational? It is argued that the next generation of the EU’s criminal justice cooperation and the EAW need to recognise and acknowledge that the mutual trust premise upon which the European system has been built so far is no longer viable without devising new EU policy stakeholders’ structures and evaluation mechanisms. These should allow for the recalibration of mutual trust and mistrust in EU justice systems in light of the experiences of the criminal justice actors and practitioners having a stake in putting the EAW into daily effect. Such a ‘bottom-up approach’ should be backed up with the best impartial and objective evaluation, an improved system of statistical collection and an independent qualitative assessment of its implementation. This should be placed as the central axis of a renewed EAW framework which should seek to better ensure the accountability, impartial (EU-led) scrutiny and transparency of member states’ application of the EAW in light of the general principles and fundamental rights constituting the foundations of the European system of criminal justice cooperation.

Biologic therapies and non-melanoma skin cancer rates in three chronic immune-mediated diseases

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

The Triangular Relationship between Fundamental Rights, Democracy and the Rule of Law in the EU: Towards an EU Copenhagen Mechanism. CEPS Paperbacks. November 2013

This study examines the protection of fundamental rights, democracy and rule of law in the European Union, and the challenges that arise in reflecting on ways to strengthen EU competences in these contested terrains. It provides a ‘state of play’ and critical account of EU-level policy and legal mechanisms assessing the relationship between rule of law, democracy and fundamental rights in the member states of the Union. The cross-cutting challenges affecting their uses, effective implementation and practical operability constitute a central point of the analysis. The study argues that the relationship between rule of law, democracy and fundamental rights is co-constitutive. Any future rule of law-related policy discussion in the EU should start from an understanding of the triangular relationship between these dimensions from the perspective of ‘democratic rule of law with fundamental rights’, i.e. the legally based rule of a democratic state that delivers fundamental rights. The three criteria are inherently and indivisibly interconnected, and interdependent on each of the others, and they cannot be separated without inflicting profound damage to the whole and changing its essential shape and configuration.

On Political Union in Europe: The changing landscape of decisionmaking and political accountability. CEPS Essay No. 4, 21 February 2013

This essay discusses how recent developments have modified the existing allocation of tasks between the EU and national levels and the legitimising mechanisms in decision-making by the EU institutions. It examines in turn the increasing differentiation emerging in member states’ participation in EU policies and institutions, the changing configuration of executive powers and its relationship to the community method, the criteria governing the transfer of economic powers from the member states to the Union and the emerging democratic accountability and legitimising mechanisms before both the European and the national parliaments. Some main implications for the future of European institutions are summarised in the conclusions.

On the initiation of boudinage and folding instabilities in layered elasto-visco-plastic solids - Insights from natural microstructures and numerical simulations

The present understanding of the initiation of boudinage and folding structures is based on viscosity contrasts and stress exponents, considering an intrinsically unstable state of the layer. The criterion of localization is believed to be prescribed by geometry-material interactions, which are often encountered in natural structures. An alternative localization phenomenon has been established for ductile materials, in which instability emerges for critical material parameters and loading rates from homogeneous conditions. In this thesis, conditions are sought under which this type of instability prevails and whether localization in geological materials necessarily requires a trigger by geometric imperfections. The relevance of critical deformation conditions, material parameters and the spatial configuration of instabilities are discussed in a geological context. In order to analyze boudinage geometries, a numerical eigenmode analysis is introduced. This method allows determining natural frequencies and wavelengths of a structure and inducing perturbations on these frequencies. In the subsequent coupled thermo-mechanical simulations, using a grain size evolution and end-member flow laws, localization emerges when material softening through grain size sensitive viscous creep sets in. Pinch-and-swell structures evolve along slip lines through a positive feedback between the matrix response and material bifurcations inside the layer, independent from the mesh-discretization length scale. Since boudinage and folding are considered to express the same general instability, both structures should arise independently of the sign of the loading conditions and for identical material parameters. To this end, the link between material to energy instabilities is approached by means of bifurcation analyses of the field equations and finite element simulations of the coupled system of equations. Boudinage and folding structures develop at the same critical energy threshold, where dissipative work by temperature-sensitive creep overcomes the diffusive capacity of the layer. This finding provides basis for a unified theory for strain localization in layered ductile materials. The numerical simulations are compared to natural pinch-and-swell microstructures, tracing the adaption of grain sizes, textures and creep mechanisms in calcite veins. The switch from dislocation to diffusion creep relates to strain-rate weakening, which is induced by dissipated heat from grain size reduction, and marks the onset of continuous necking. The time-dependent sequence uncovers multiple steady states at different time intervals. Microstructurally and mechanically stable conditions are finally expressed in the pinch-and-swell end members. The major outcome of this study is that boudinage and folding can be described as the same coupled energy-mechanical bifurcation, or as one critical energy attractor. This finding allows the derivation of critical deformation conditions and fundamental material parameters directly from localized structures in the field.

(Table 19, page 199) Minor constituents of one of the San Clemente iron concretions and its metallic core

The chemical and mineralogical composition of pelagic sediments from the East Pacific Ocean has been determined with the aim of defining the ultimate sources and the mechanisms of formation of the solid phases. The distribution of elements between sea-water, the pore solution and the various solid components of the sediments permits interpretations of the variations in time and space of the gross chemical composition of pelagic clays. For example, manganese, present in sea-water in a divalent form, is apparently oxidized at the sediment-water interface to tetravalent species which subsequently become a part of the group of ferromanganese oxide minerals which are found in the marine environment. It is suggested the rate of manganese accumulation in sediments is some function of the length of time the sediment surface is in contact with sea-water. The contribution of chemical species from the different geospheres is considered. The quantitative importance of pelagic clays in the major sedimentary cycle is studied on the basis of the distribution of the weathered igneous rock products between continental and pelagic deposits and sea-water. These analyses of a wide variety of pelagic clays allow a reformulation of the geochemical balance and it is concluded that pelagic clays account for approximately 13 per cent of the total mass of sediments produced over geologic time.

Spatial distribution and morphometric analysis of thermokarst lakes and other water bodies : Case study from the sporadic permafrost region, Tavvavuoma, Sweden

Projected air and ground temperatures are expected to be higher in Arctic and sub-Arcticlatitudes and with temperatures already close to the limit where permafrost can exist,resistance against degradation is low. With thawing permafrost, the landscape is modifiedwith depression in which thermokarst lakes emerge. In permafrost soils a considerableamount of soil organic carbon is stored, with the potential of altering climate even furtherif expansion and formation of new thermokarst lakes emerge, as decay releasesgreenhouse gases (C02 and CH4) to the atmosphere. Analyzing the spatial distribution andmorphometry over time of thermokarst lakes and other water bodies, is of importance inaccurately predict carbon budget and feedback mechanisms, as well as to assess futurelandscape layout and these features interaction. Different types of high-spatial resolutionaerial and satellite imageries from 1963, 1975, 2003, 2010 and 2015, were used in bothpre- and post-classification change detection analyses. Using object oriented segmentationin eCognition combined with manual adjustments, resulted in digitalized water bodies>28m2 from which direction of change and morphometric values were extracted. Thequantity of thermokarst lakes and other water bodies was in 1963 n=92, with succeedingyears as a trend decreased in numbers, until 2010-2015 when eleven water bodies wereadded in 2015 (n=74 to n=85). In 1963-2003, area of these water bodies decreased with50 651m2 (189 446-138 795m2) and continued to decrease in 2003-2015 ending at 129337m2. Limnicity decreased from 19.9% in 1963 to 14.6% in 2003 (-5.3%). In 2010 and2015 13.7-13.6%. The late increase in water bodies differs from an earlier hypothesis thatsporadic permafrost regions experience decrease in both area and quantity of thermokarstlakes and water bodies. During 1963-2015, land gain has been in dominance of the ratiobetween the two competing processes of expansion and drainage. In 1963-1975, 55/45%,followed by 90/10% in 1975-2003. After major drainage events, land loss increased to62/38% in 2010-2015. Drainage and infilling rates, calculated for 15 shorelines werevaried across both landscape and parts of shorelines, with in average 0.17/0.15/0.14m/yr.Except for 1963-1975 when rate of change in average was in opposite direction (-0.09m/yr.), likely due to evident expansion of a large thermokarst lake. Using a squaregrid, distribution of water bodies was determined, with an indistinct cluster located in NEand central parts. Especially for water bodies <250m2, which is the dominant area classthroughout 1963-2015 ranging from n=39-51. With a heterogeneous composition of bothsmall and large thermokarst lakes, and with both expansion and drainage altering thelandscape in Tavvavuoma, both positive and negative climate feedback mechanisms are inplay - given that sporadic permafrost still exist.

The relationship between non-orthographic language abilities and reading performance: An exploration of the primary systems hypothesis in chronic aphasia

Thesis (Ph.D.)--University of Washington, 2016-06

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km x 10 km rolled transects are used to approximate a 500 km x 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

Mechanism of adhesion and detachment at the anterior end of Neoheterocotyle rhinobatidis and Troglocephalus rhinobatidis (Monogenea : Monopisthocotylea : Monocotylidae)

The anterior adhesion and detachment mechanisms observed for Neoheterocotyle rhinobatidis and Troglocephalus rhinobatidis (Monogenea: Monocotylidae) appear similar to those observed for the two other monopisthocotylean monogenean species with anterior apertures for which published data are available. This supports the theory that monogeneans with apertures may utilise a common mechanism. Adult anterior apertures can open and close and duct endings can evert during the adhesion phase and retract during detachment and searching behaviour. The adhesive is comprised of two secretory types, rod-shaped and spheroidal bodies, found within anterior apertures. These exit together and undergo mixing to produce the adhesive matrix in which elongate membranes from rod-shaped bodies are seen intermixed with a granular electron-dense matrix. The morphology of the adhesive matrix differs from that found for some other monogenean taxa. Anterior detachment by these monocotylids appears to involve a depletion of rod-shaped bodies in ducts and mechanical withdrawal of the anterior end.

5 '-Untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation

Upstream AUGs (uAUGs) and upstream open reading frames (uORFs) are common features of mRNAs that encode regulatory proteins and have been shown to profoundly influence translation of the main ORF. In this study, we employed a series of artificial 5'-untranslated regions (5'-UTRs) containing one or more uAUGs/uORFs to systematically assess translation initiation at the main AUG by leaky scanning and reinitiation mechanisms. Constructs containing either one or two uAUGs in varying contexts but without an in-frame stop codon upstream of the main AUG were used to analyse the leaky scanning mechanism. This analysis largely confirmed the ranking of different AUG contextual sequences that was determined previously by Kozak. In addition, this ranking was the same for both the first and second uAUGs, although the magnitude of initiation efficiency differed. Moreover, similar to10% of ribosomes exhibited leaky scanning at uAUGs in the most favourable context and initiated at a downstream AUG. A second group of constructs containing different numbers of uORFs, each with optimal uAUGs, were used to measure the capacity for reinitiation. We found significant levels of initiation at the main ORF even in constructs containing four uORFs, with nearly 10% of ribosomes capable of reinitiating five times. This study shows that for mRNAs containing multiple uORFs/uAUGs, ribosome reinitiation and leaky scanning are efficient mechanisms for initiation at their main AUGs.