High power beam dump project for the accelerator prototype LIPAc: Cooling design and analysis

En el campo de la fusión nuclear y desarrollándose en paralelo a ITER (International Thermonuclear Experimental Reactor), el proyecto IFMIF (International Fusion Material Irradiation Facility) se enmarca dentro de las actividades complementarias encaminadas a solucionar las barreras tecnológicas que aún plantea la fusión. En concreto IFMIF es una instalación de irradiación cuya misión es caracterizar materiales resistentes a condiciones extremas como las esperadas en los futuros reactores de fusión como DEMO (DEMOnstration power plant). Consiste de dos aceleradores de deuterones que proporcionan un haz de 125 mA y 40 MeV cada uno, que al colisionar con un blanco de litio producen un flujo neutrónico intenso (1017 neutrones/s) con un espectro similar al de los neutrones de fusión [1], [2]. Dicho flujo neutrónico es empleado para irradiar los diferentes materiales candidatos a ser empleados en reactores de fusión, y las muestras son posteriormente examinadas en la llamada instalación de post-irradiación. Como primer paso en tan ambicioso proyecto, una fase de validación y diseño llamada IFMIFEVEDA (Engineering Validation and Engineering Design Activities) se encuentra actualmente en desarrollo. Una de las actividades contempladas en esta fase es la construcción y operación de una acelarador prototipo llamado LIPAc (Linear IFMIF Prototype Accelerator). Se trata de un acelerador de deuterones de alta intensidad idéntico a la parte de baja energía de los aceleradores de IFMIF. Los componentes del LIPAc, que será instalado en Japón, son suministrados por diferentes países europeos. El acelerador proporcionará un haz continuo de deuterones de 9 MeV con una potencia de 1.125 MW que tras ser caracterizado con diversos instrumentos deberá pararse de forma segura. Para ello se requiere un sistema denominado bloque de parada (Beam Dump en inglés) que absorba la energía del haz y la transfiera a un sumidero de calor. España tiene el compromiso de suministrar este componente y CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) es responsable de dicha tarea. La pieza central del bloque de parada, donde se para el haz de iones, es un cono de cobre con un ángulo de 3.5o, 2.5 m de longitud y 5 mm de espesor. Dicha pieza está refrigerada por agua que fluye en su superficie externa por el canal que se forma entre el cono de cobre y otra pieza concéntrica con éste. Este es el marco en que se desarrolla la presente tesis, cuyo objeto es el diseño del sistema de refrigeración del bloque de parada del LIPAc. El diseño se ha realizado utilizando un modelo simplificado unidimensional. Se han obtenido los parámetros del agua (presión, caudal, pérdida de carga) y la geometría requerida en el canal de refrigeración (anchura, rugosidad) para garantizar la correcta refrigeración del bloque de parada. Se ha comprobado que el diseño permite variaciones del haz respecto a la situación nominal siendo el flujo crítico calorífico al menos 2 veces superior al nominal. Se han realizado asimismo simulaciones fluidodinámicas 3D con ANSYS-CFX en aquellas zonas del canal de refrigeración que lo requieren. El bloque de parada se activará como consecuencia de la interacción del haz de partículas lo que impide cualquier cambio o reparación una vez comenzada la operación del acelerador. Por ello el diseño ha de ser muy robusto y todas las hipótesis utilizadas en la realización de éste deben ser cuidadosamente comprobadas. Gran parte del esfuerzo de la tesis se centra en la estimación del coeficiente de transferencia de calor que es determinante en los resultados obtenidos, y que se emplea además como condición de contorno en los cálculos mecánicos. Para ello por un lado se han buscado correlaciones cuyo rango de aplicabilidad sea adecuado para las condiciones del bloque de parada (canal anular, diferencias de temperatura agua-pared de decenas de grados). En un segundo paso se han comparado los coeficientes de película obtenidos a partir de la correlación seleccionada (Petukhov-Gnielinski) con los que se deducen de simulaciones fluidodinámicas, obteniendo resultados satisfactorios. Por último se ha realizado una validación experimental utilizando un prototipo y un circuito hidráulico que proporciona un flujo de agua con los parámetros requeridos en el bloque de parada. Tras varios intentos y mejoras en el experimento se han obtenido los coeficientes de película para distintos caudales y potencias de calentamiento. Teniendo en cuenta la incertidumbre de las medidas, los valores experimentales concuerdan razonablemente bien (en el rango de 15%) con los deducidos de las correlaciones. Por motivos radiológicos es necesario controlar la calidad del agua de refrigeración y minimizar la corrosión del cobre. Tras un estudio bibliográfico se identificaron los parámetros del agua más adecuados (conductividad, pH y concentración de oxígeno disuelto). Como parte de la tesis se ha realizado asimismo un estudio de la corrosión del circuito de refrigeración del bloque de parada con el doble fin de determinar si puede poner en riesgo la integridad del componente, y de obtener una estimación de la velocidad de corrosión para dimensionar el sistema de purificación del agua. Se ha utilizado el código TRACT (TRansport and ACTivation code) adaptándalo al caso del bloque de parada, para lo cual se trabajó con el responsable (Panos Karditsas) del código en Culham (UKAEA). Los resultados confirman que la corrosión del cobre en las condiciones seleccionadas no supone un problema. La Tesis se encuentra estructurada de la siguiente manera: En el primer capítulo se realiza una introducción de los proyectos IFMIF y LIPAc dentro de los cuales se enmarca esta Tesis. Además se describe el bloque de parada, siendo el diseño del sistema de rerigeración de éste el principal objetivo de la Tesis. En el segundo y tercer capítulo se realiza un resumen de la base teórica así como de las diferentes herramientas empleadas en el diseño del sistema de refrigeración. El capítulo cuarto presenta los resultados del relativos al sistema de refrigeración. Tanto los obtenidos del estudio unidimensional, como los obtenidos de las simulaciones fluidodinámicas 3D mediante el empleo del código ANSYS-CFX. En el quinto capítulo se presentan los resultados referentes al análisis de corrosión del circuito de refrigeración del bloque de parada. El capítulo seis se centra en la descripción del montaje experimental para la obtención de los valores de pérdida de carga y coeficiente de transferencia del calor. Asimismo se presentan los resultados obtenidos en dichos experimentos. Finalmente encontramos un capítulo de apéndices en el que se describen una serie de experimentos llevados a cabo como pasos intermedios en la obtención del resultado experimental del coeficiente de película. También se presenta el código informático empleado para el análisis unidimensional del sistema de refrigeración del bloque de parada llamado CHICA (Cooling and Heating Interaction and Corrosion Analysis). ABSTRACT In the nuclear fusion field running in parallel to ITER (International Thermonuclear Experimental Reactor) as one of the complementary activities headed towards solving the technological barriers, IFMIF (International Fusion Material Irradiation Facility) project aims to provide an irradiation facility to qualify advanced materials resistant to extreme conditions like the ones expected in future fusion reactors like DEMO (DEMOnstration Power Plant). IFMIF consists of two constant wave deuteron accelerators delivering a 125 mA and 40 MeV beam each that will collide on a lithium target producing an intense neutron fluence (1017 neutrons/s) with a similar spectra to that of fusion neutrons [1], [2]. This neutron flux is employed to irradiate the different material candidates to be employed in the future fusion reactors, and the samples examined after irradiation at the so called post-irradiative facilities. As a first step in such an ambitious project, an engineering validation and engineering design activity phase called IFMIF-EVEDA (Engineering Validation and Engineering Design Activities) is presently going on. One of the activities consists on the construction and operation of an accelerator prototype named LIPAc (Linear IFMIF Prototype Accelerator). It is a high intensity deuteron accelerator identical to the low energy part of the IFMIF accelerators. The LIPAc components, which will be installed in Japan, are delivered by different european countries. The accelerator supplies a 9 MeV constant wave beam of deuterons with a power of 1.125 MW, which after being characterized by different instruments has to be stopped safely. For such task a beam dump to absorb the beam energy and take it to a heat sink is needed. Spain has the compromise of delivering such device and CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) is responsible for such task. The central piece of the beam dump, where the ion beam is stopped, is a copper cone with an angle of 3.5o, 2.5 m long and 5 mm width. This part is cooled by water flowing on its external surface through the channel formed between the copper cone and a concentric piece with the latter. The thesis is developed in this realm, and its objective is designing the LIPAc beam dump cooling system. The design has been performed employing a simplified one dimensional model. The water parameters (pressure, flow, pressure loss) and the required annular channel geometry (width, rugoisty) have been obtained guaranteeing the correct cooling of the beam dump. It has been checked that the cooling design allows variations of the the beam with respect to the nominal position, being the CHF (Critical Heat Flux) at least twice times higher than the nominal deposited heat flux. 3D fluid dynamic simulations employing ANSYS-CFX code in the beam dump cooling channel sections which require a more thorough study have also been performed. The beam dump will activateasaconsequenceofthe deuteron beam interaction, making impossible any change or maintenance task once the accelerator operation has started. Hence the design has to be very robust and all the hypotheses employed in the design mustbecarefully checked. Most of the work in the thesis is concentrated in estimating the heat transfer coefficient which is decisive in the obtained results, and is also employed as boundary condition in the mechanical analysis. For such task, correlations which applicability range is the adequate for the beam dump conditions (annular channel, water-surface temperature differences of tens of degrees) have been compiled. In a second step the heat transfer coefficients obtained from the selected correlation (Petukhov- Gnielinski) have been compared with the ones deduced from the 3D fluid dynamic simulations, obtaining satisfactory results. Finally an experimental validation has been performed employing a prototype and a hydraulic circuit that supplies a flow with the requested parameters in the beam dump. After several tries and improvements in the experiment, the heat transfer coefficients for different flows and heating powers have been obtained. Considering the uncertainty in the measurements the experimental values agree reasonably well (in the order of 15%) with the ones obtained from the correlations. Due to radiological reasons the quality of the cooling water must be controlled, hence minimizing the copper corrosion. After performing a bibligraphic study the most adequate water parameters were identified (conductivity, pH and dissolved oxygen concentration). As part of this thesis a corrosion study of the beam dump cooling circuit has been performed with the double aim of determining if corrosion can pose a risk for the copper beam dump , and obtaining an estimation of the corrosion velocitytodimension the water purification system. TRACT code(TRansport and ACTivation) has been employed for such study adapting the code for the beam dump case. For such study a collaboration with the code responsible (Panos Karditsas) at Culham (UKAEA) was established. The work developed in this thesis has supposed the publication of three articles in JCR journals (”Journal of Nuclear Materials” y ”Fusion Engineering and Design”), as well as presentations in more than four conferences and relevant meetings.

Stability Analysis of Teleoperation System by State Convergence with Variable Time Delay

We propose a novel control scheme for bilateral teleoperation of n degree-of-freedom (DOF) nonlinear robotic systems with time-varying communication delay. A major contribution from this work lies in the demonstration that the structure of a state convergence algorithm can be also applied to nth-order nonlinear teleoperation systems. By choosing a Lyapunov Krasovskii functional, we show that the local-remote teleoperation system is asymptotically stable. The time delay of communication channel is assumed to be unknown and randomly time varying, but the upper bounds of the delay interval and the derivative of the delay are assumed to be known.

A multi-scale analysis of transforming agricultural markets in the context of globalization: implications for natural resources, food prices and rural poverty in Latin America

Vivimos una época en la que el mundo se transforma aceleradamente. La globalización está siguiendo un curso imparable, la población mundial así como la población urbana siguen creciendo, y en los países emergentes los ingresos promedios aumentan, resultando en un cambio también acelerado de las dietas y hábitos alimentarios. En conjunto esos factores están causando un aumento fundamental de la demanda de alimentos. Junto con la apertura de los mercados agrícolas, estos procesos han provocado un crecimiento del comercio internacional de alimentos durante la última década. Dado que muchos países de América Latina están dotados de abundancia de recursos naturales, estas tendencias han producido un crecimiento rápido de las exportaciones de bienes primarios desde América Latina al resto del mundo. En sólo 30 años la participación en el mercado agrícola de América Latina casi se ha duplicado, desde 10% en 1980 a 18% en 2010. Este aumento del comercio agrícola ha dado lugar a un debate sobre una serie de cuestiones cruciales relacionadas con los impactos del comercio en la seguridad alimentaria mundial, en el medio ambiente o en la reducción de la pobreza rural en países en desarrollo. Esta tesis aplica un marco integrado para analizar varios impactos relacionados con la transformación de los mercados agrícolas y los mercados rurales debidos a la globalización y, en particular, al progresivo aumento del comercio internacional. En concreto, la tesis aborda los siguientes temas: En primer lugar, la producción mundial de alimentos tendrá que aumentar considerablemente para poder satisfacer la demanda de una población mundial de 9000 millones personas en 2050, lo cual plantea grandes desafíos sobre los sistemas de la producción de alimentos. Alcanzar este logro, sin comprometer la integridad del medio ambiente en regiones exportadoras, es un reto aún mayor. En este contexto, la tesis analiza los efectos de la liberalización del comercio mundial, considerando distintas tecnologías de producción agraria, sobre unos indicadores de seguridad alimentaria en diferentes regiones del mundo y sobre distintos indicadores ambientales, teniendo en cuenta escalas diferentes en América Latina y el Caribe. La tesis utiliza el modelo “International Model for Policy Analysis of Agricultural Commodities and Trade (IMPACT)” – un modelo dinámico de equilibrio parcial del sector agrícola a escala global – para modelar la apertura de los mercados agrícolas así como diferentes escenarios de la producción hasta el año 2050. Los resultados del modelo están vinculados a modelos biofísicos para poder evaluar los cambios en la huella hídrica y la calidad del agua, así como para cuantificar los impactos del cambio en el uso del suelo sobre la biodiversidad y los stocks de carbono en 2050. Los resultados indican que la apertura de los mercados agrícolas es muy importante para mejorar la seguridad alimentaria a nivel mundial, sin embargo, produce también presiones ambientales indeseables en algunas regiones de América Latina. Contrastando dos escenarios que consideran distintas modos de producción, la expansión de la tierra agrícola frente a un escenario de la producción más intensiva, se demuestra que las mejoras de productividad son generalmente superiores a la expansión de las tierras agrícolas, desde un punto de vista económico e ambiental. En cambio, los escenarios de intensificación sostenible no sólo hacen posible una mayor producción de alimentos, sino que también generan menos impactos medioambientales que los otros escenarios futuros en todas sus dimensiones: biodiversidad, carbono, emisiones de nitratos y uso del agua. El análisis muestra que hay un “trade-off” entre el objetivo de alcanzar la sostenibilidad ambiental y el objetivo de la seguridad alimentaria, independiente del manejo agrícola en el futuro. En segundo lugar, a la luz de la reciente crisis de los precios de alimentos en los años 2007/08, la tesis analiza los impactos de la apertura de los mercados agrícolas en la transmisión de precios de los alimentos en seis países de América Latina: Argentina, Brasil, Chile, Colombia, México y el Perú. Para identificar las posibles relaciones de cointegración entre los índices de precios al consumidor de alimentos y los índices de precios de agrarios internacionales, sujetos a diferentes grados de apertura de mercados agrícolas en los seis países de América Latina, se utiliza un modelo simple de corrección de error (single equation error correction). Los resultados indican que la integración global de los mercados agrícolas ha dado lugar a diferentes tasas de transmisión de precios en los países investigados. Sobre todo en el corto plazo, las tasas de transmisión dependen del grado de apertura comercial, mientras que en el largo plazo las tasas de transmisión son elevadas, pero en gran medida independientes del régimen de comercio. Por lo tanto, durante un período de shocks de precios mundiales una mayor apertura del comercio trae consigo más inestabilidad de los precios domésticos a corto plazo y la resultante persistencia en el largo plazo. Sin embargo, estos resultados no verifican necesariamente la utilidad de las políticas comerciales, aplicadas frecuentemente por los gobiernos para amortiguar los shocks de precios. Primero, porque existe un riesgo considerable de volatilidad de los precios debido a cambios bruscos de la oferta nacional si se promueve la autosuficiencia en el país; y segundo, la política de proteccionismo asume el riesgo de excluir el país de participar en las cadenas de suministro de alto valor del sector agrícola, y por lo tanto esa política podría obstaculizar el desarrollo económico. Sin embargo, es indispensable establecer políticas efectivas para reducir la vulnerabilidad de los hogares a los aumentos repentinos de precios de alimentos, lo cual requiere una planificación gubernamental precisa con el presupuesto requerido disponible. En tercer lugar, la globalización afecta a la estructura de una economía y, por medios distintos, la distribución de los ingreso en un país. Perú sirve como ejemplo para investigar más profundamente las cuestiones relacionadas con los cambios en la distribución de los ingresos en zonas rurales. Perú, que es un país que está cada vez más integrado en los mercados mundiales, consiguió importantes descensos en la pobreza extrema en sus zonas rurales, pero a la vez adolece de alta incidencia de pobreza moderada y de desigualdad de los ingresos en zonas rural al menos durante el periodo comprendido entre 2004 y 2012. Esta parte de la tesis tiene como objetivo identificar las fuerzas impulsoras detrás de estas dinámicas en el Perú mediante el uso de un modelo de microsimulación basado en modelos de generación de ingresos aplicado a nivel los hogares rurales. Los resultados indican que la fuerza principal detrás de la reducción de la pobreza ha sido el crecimiento económico general de la economía, debido a las condiciones macroeconómicas favorables durante el periodo de estudio. Estos efectos de crecimiento beneficiaron a casi todos los sectores rurales, y dieron lugar a la disminución de la pobreza rural extrema, especialmente entre los agricultores de papas y de maíz. En parte, estos agricultores probablemente se beneficiaron de la apertura de los mercados agrícolas, que es lo que podría haber provocado un aumento de los precios al productor en tiempos de altos precios mundiales de los alimentos. Sin embargo, los resultados también sugieren que para una gran parte de la población más pobre existían barreras de entrada a la hora de poder participar en el empleo asalariado fuera de la agricultura o en la producción de cultivos de alto valor. Esto podría explicarse por la falta de acceso a unos activos importantes: por ejemplo, el nivel de educación de los pobres era apenas mejor en 2012 que en 2004; y también las dotaciones de tierra y de mano de obra, sobre todo de los productores pobres de maíz y patata, disminuyeron entre 2004 y 2012. Esto lleva a la conclusión de que aún hay margen para aplicar políticas para facilitar el acceso a estos activos, que podría contribuir a la erradicación de la pobreza rural. La tesis concluye que el comercio agrícola puede ser un importante medio para abastecer una población mundial creciente y más rica con una cantidad suficiente de calorías. Para evitar adversos efectos ambientales e impactos negativos para los consumidores y de los productores pobres, el enfoque debe centrarse en las mejoras de la productividad agrícola, teniendo en cuenta los límites ambientales y ser socialmente inclusivo. En este sentido, será indispensable seguir desarrollando soluciones tecnológicas que garanticen prácticas de producción agrícola minimizando el uso de recursos naturales. Además, para los pequeños pobres agricultores será fundamental eliminar las barreras de entrada a los mercados de exportación que podría tener efectos indirectos favorables a través de la adopción de nuevas tecnologías alcanzables a través de mercados internacionales. ABSTRACT The world is in a state of rapid transition. Ongoing globalization, population growth, rising living standards and increasing urbanization, accompanied by changing dietary patterns throughout the world, are increasing the demand for food. Together with more open trade regimes, this has triggered growing international agricultural trade during the last decade. For many Latin American countries, which are gifted with relative natural resource abundance, these trends have fueled rapid export growth of primary goods. In just 30 years, the Latin American agricultural market share has almost doubled from 10% in 1980 to 18% in 2010. These market developments have given rise to a debate around a number of crucial issues related to the role of agricultural trade for global food security, for the environment or for poverty reduction in developing countries. This thesis uses an integrated framework to analyze a broad array of possible impacts related to transforming agricultural and rural markets in light of globalization, and in particular of increasing trade activity. Specifically, the following issues are approached: First, global food production will have to rise substantially by the year 2050 to meet effective demand of a nine billion people world population which poses major challenges to food production systems. Doing so without compromising environmental integrity in exporting regions is an even greater challenge. In this context, the thesis explores the effects of future global trade liberalization on food security indicators in different world regions and on a variety of environmental indicators at different scales in Latin America and the Caribbean, in due consideration of different future agricultural production practices. The International Model for Policy Analysis of Agricultural Commodities and Trade (IMPACT) –a global dynamic partial equilibrium model of the agricultural sector developed by the International Food Policy Research Institute (IFPRI)– is applied to run different future production scenarios, and agricultural trade regimes out to 2050. Model results are linked to biophysical models, used to assess changes in water footprints and water quality, as well as impacts on biodiversity and carbon stocks from land use change by 2050. Results indicate that further trade liberalization is crucial for improving food security globally, but that it would also lead to more environmental pressures in some regions across Latin America. Contrasting land expansion versus more intensified agriculture shows that productivity improvements are generally superior to agricultural land expansion, from an economic and environmental point of view. Most promising for achieving food security and environmental goals, in equal measure, is the sustainable intensification scenario. However, the analysis shows that there are trade-offs between environmental and food security goals for all agricultural development paths. Second, in light of the recent food price crisis of 2007/08, the thesis looks at the impacts of increasing agricultural market integration on food price transmission from global to domestic markets in six Latin American countries, namely Argentina, Brazil, Chile, Colombia, Mexico and Peru. To identify possible cointegrating relationships between the domestic food consumer price indices and world food price levels, subject to different degrees of agricultural market integration in the six Latin American countries, a single equation error correction model is used. Results suggest that global agricultural market integration has led to different levels of price path-through in the studied countries. Especially in the short-run, transmission rates depend on the degree of trade openness, while in the long-run transmission rates are high, but largely independent of the country-specific trade regime. Hence, under world price shocks more trade openness brings with it more price instability in the short-term and the resulting persistence in the long-term. However, these findings do not necessarily verify the usefulness of trade policies, often applied by governments to buffer such price shocks. First, because there is a considerable risk of price volatility due to domestic supply shocks if self-sufficiency is promoted. Second, protectionism bears the risk of excluding a country from participating in beneficial high-value agricultural supply chains, thereby hampering economic development. Nevertheless, to reduce households’ vulnerability to sudden and large increases of food prices, effective policies to buffer food price shocks should be put in place, but must be carefully planned with the required budget readily available. Third, globalization affects the structure of an economy and, by different means, the distribution of income in a country. Peru serves as an example to dive deeper into questions related to changes in the income distribution in rural areas. Peru, a country being increasingly integrated into global food markets, experienced large drops in extreme rural poverty, but persistently high rates of moderate rural poverty and rural income inequality between 2004 and 2012. The thesis aims at disentangling the driving forces behind these dynamics by using a microsimulation model based on rural household income generation models. Results provide evidence that the main force behind poverty reduction was overall economic growth of the economy due to generally favorable macroeconomic market conditions. These growth effects benefited almost all rural sectors, and led to declines in extreme rural poverty, especially among potato and maize farmers. In part, these farmers probably benefited from policy changes towards more open trade regimes and the resulting higher producer prices in times of elevated global food price levels. However, the results also suggest that entry barriers existed for the poorer part of the population to participate in well-paid wage-employment outside of agriculture or in high-value crop production. This could be explained by a lack of sufficient access to important rural assets. For example, poor people’s educational attainment was hardly better in 2012 than in 2004. Also land and labor endowments, especially of (poor) maize and potato growers, rather decreased than increased over time. This leads to the conclusion that there is still scope for policy action to facilitate access to these assets, which could contribute to the eradication of rural poverty. The thesis concludes that agricultural trade can be one important means to provide a growing and richer world population with sufficient amounts of calories. To avoid adverse environmental effects and negative impacts for poor food consumers and producers, the focus should lie on agricultural productivity improvements, considering environmental limits and be socially inclusive. In this sense, it will be crucial to further develop technological solutions that guarantee resource-sparing agricultural production practices, and to remove entry barriers for small poor farmers to export markets which might allow for technological spill-over effects from high-value global agricultural supply chains.

Identification and analysis of the plant peroxisomal targeting signal 1 receptor NtPEX5

Protein translocation into peroxisomes takes place via recognition of a peroxisomal targeting signal present at either the extreme C termini (PTS1) or N termini (PTS2) of matrix proteins. In mammals and yeast, the peroxisomal targeting signal receptor, Pex5p, recognizes the PTS1 consisting of -SKL or variants thereof. Although many plant peroxisomal matrix proteins are transported through the PTS1 pathway, little is known about the PTS1 receptor or any other peroxisome assembly protein from plants. We cloned tobacco (Nicotiana tabacum) cDNAs encoding Pex5p (NtPEX5) based on the protein’s interaction with a PTS1-containing protein in the yeast two-hybrid system. Nucleotide sequence analysis revealed that the tobacco Pex5p contains seven tetratricopeptide repeats and that NtPEX5 shares greater sequence similarity with its homolog from humans than from yeast. Expression of NtPEX5 fusion proteins, consisting of the N-terminal part of yeast Pex5p and the C-terminal region of NtPEX5, in a Saccharomyces cerevisiae pex5 mutant restored protein translocation into peroxisomes. These experiments confirmed the identity of the tobacco protein as a PTS1 receptor and indicated that components of the peroxisomal translocation apparatus are conserved functionally. Two-hybrid assays showed that NtPEX5 interacts with a wide range of PTS1 variants that also interact with the human Pex5p. Interestingly, the C-terminal residues of some of these peptides deviated from the established plant PTS1 consensus sequence. We conclude that there are significant sequence and functional similarities between the plant and human Pex5ps.

Genomic and cDNA sequence analysis of the cell matrix adhesion regulator gene

The cell matrix adhesion regulator (CMAR) gene has been suggested to be a signal transduction molecule influencing cell adhesion to collagen and, through this, possibly involved in tumor suppression. The originally reported CMAR cDNA was 464 bp long with a tyrosine phosphorylation site at the extreme 3′ end, which mutagenesis studies had shown to be central to the function of this gene. Since the discovery of a 4-bp insertion polymorphism within the originally reported coding region, further sequence information has been obtained. The cDNA has been extended 5′ by ≈2 kb revealing a 559-bp region showing strong homology to the proposed 5′ untranslated sequence of a murine protein kinase receptor family member, variant in kinase (vik). CMAR genomic sequencing has shown the presence of an intron, the intron/exon boundary lying within this region of homology. An RNA transcript for CMAR of ≈2.5 kb has also been identified. The data suggest complex mechanisms for control of expression of two closely associated genes, CMAR and the vik- associated sequence.

The paradox of alloreactivity and self MHC restriction: Quantitative analysis and statistics

Although 1–24% of T cells are alloreactive, i.e., respond to MHC molecules encoded by a foreign haplotype, it is generally believed that T cells cannot recognize foreign peptides binding foreign MHC molecules. We show using a quantitative model that, if T cell selection and activation are affinity-driven, then an alloreactivity of 1–24% is incompatible with the textbook notion that self MHC restriction is absolute. If an average of 1% of clones are alloreactive, then according to our model, at most 20-fold more clones should, on average, be activated by antigens presented on self MHC than by antigens presented on foreign MHC. This ratio is at best 5 if alloreactivity is 5%. These results describe average properties of the murine immune system, but not the outcome of individual experiments. Using supercomputer technology, we simulated 100,000 MHC restriction experiments. Although the average restriction ratio was 7.1, restriction was absolute in 10% of the simulated experiments, greater than 100, although not absolute, in 29%, and below 6 in 24%. This extreme variability agrees with experimental estimates. Our analysis suggests that alloreactivity and average self MHC restriction both cannot be high, but that a low average restriction level is compatible with high levels in a significant number of experiments.

Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations

We report the genetic organisation of six prophages present in the genome of Lactococcus lactis IL1403. The three larger prophages (36–42 kb), belong to the already described P335 group of temperate phages, whereas the three smaller ones (13–15 kb) are most probably satellites relying on helper phage(s) for multiplication. These data give a new insight into the genetic structure of lactococcal phage populations. P335 temperate phages have variable genomes, sharing homology over only 10–33% of their length. In contrast, virulent phages have highly similar genomes sharing homology over >90% of their length. Further analysis of genetic structure in all known groups of phages active on other bacterial hosts such as Escherichia coli, Bacillus subtilis, Mycobacterium and Streptococcus thermophilus confirmed the existence of two types of genetic structure related to the phage way of life. This might reflect different intensities of horizontal DNA exchange: low among purely virulent phages and high among temperate phages and their lytic homologues. We suggest that the constraints on genetic exchange among purely virulent phages reflect their optimal genetic organisation, adapted to a more specialised and extreme form of parasitism than temperate/lytic phages.

Genetic fidelity under harsh conditions: Analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius

Microbes whose genomes are encoded by DNA and for which adequate information is available display similar genomic mutation rates (average 0.0034 mutations per chromosome replication, range 0.0025 to 0.0046). However, this value currently is based on only a few well characterized microbes reproducing within a narrow range of environmental conditions. In particular, no genomic mutation rate has been determined either for a microbe whose natural growth conditions may extensively damage DNA or for any member of the archaea, a prokaryotic lineage deeply diverged from both bacteria and eukaryotes. Both of these conditions are met by the extreme thermoacidophile Sulfolobus acidocaldarius. We determined the genomic mutation rate for this species when growing at pH 3.5 and 75°C based on the rate of forward mutation at the pyrE gene and the nucleotide changes identified in 101 independent mutants. The observed value of about 0.0018 extends the range of DNA-based microbes with rates close to the standard rate simultaneously to an archaeon and to an extremophile whose cytoplasmic pH and normal growth temperature greatly accelerate the spontaneous decomposition of DNA. The mutations include base pair substitutions (BPSs) and additions and deletions of various sizes, but the S. acidocaldarius spectrum differs from those of other DNA-based organisms in being relatively poor in BPSs. The paucity of BPSs cannot yet be explained by known properties of DNA replication or repair enzymes of Sulfolobus spp. It suggests, however, that molecular evolution per genome replication may proceed more slowly in S. acidocaldarius than in other DNA-based organisms examined to date.

Electoral Systems and Ethnic Conciliation: A Structured, Focused Analysis of Vote-Pooling in Northern Ireland Elections 1998-2011

This research project examines the role of electoral system rules in affecting the extent of conciliatory behavior and cross-ethnic coalition making in Northern Ireland. It focuses on the role of the Single Transferable Vote (STV) electoral system in shaping party and voter incentives in a post-conflict divided society. The research uses a structured, focused comparison of the four electoral cycles since the Belfast Agreement of 1998. This enables a systematic examination of each electoral cycle using a common set of criteria focused on conciliation and cross-ethnic coalition making. Whilst preference voting is assumed to benefit moderate candidates, in Northern Ireland centrist and multi-ethnic parties outside of the dominant ethnic communities have received little electoral success. In Northern Ireland the primary effect of STV has not been to encourage inter-communal voting but to facilitate intra-community and intra-party moderation. STV has encouraged the moderation of the historically extreme political parties in each of the ethnic bloc. Patterns across electoral cycles suggest that party elites from the Democratic Unionist Party (DUP) and Sinn Fein have moderated their policy positions due to the electoral system rules. Therefore they have pursued lower-preference votes from within their ethnic bloc but in doing so have marginalized parties of a multi-ethnic or non-ethnic orientation.

Missing Rings in Pinus halepensis – The Missing Link to Relate the Tree-Ring Record to Extreme Climatic Events

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of a tree ring is largely determined by the rate and duration of cell division by the vascular cambium. In the Mediterranean climate, this division may occur throughout almost the entire year. Alternatively, cell division may cease during relatively cool and dry winters, only to resume in the same calendar year with milder temperatures and increased availability of water. Under particularly adverse conditions, no xylem may be produced in parts of the stem, resulting in a missing ring (MR). A dendrochronological network of Pinus halepensis was used to determine the relationship of MR to ECE. The network consisted of 113 sites, 1,509 trees, 2,593 cores, and 225,428 tree rings throughout the distribution range of the species. A total of 4,150 MR were identified. Binomial logistic regression analysis determined that MR frequency increased with increased cambial age. Spatial analysis indicated that the geographic areas of south-eastern Spain and northern Algeria contained the greatest frequency of MR. Dendroclimatic regression analysis indicated a non-linear relationship of MR to total monthly precipitation and mean temperature. MR are strongly associated with the combination of monthly mean temperature from previous October till current February and total precipitation from previous September till current May. They are likely to occur with total precipitation lower than 50 mm and temperatures higher than 5°C. This conclusion is global and can be applied to every site across the distribution area. Rather than simply being a complication for dendrochronology, MR formation is a fundamental response of trees to adverse environmental conditions. The demonstrated relationship of MR formation to ECE across this dendrochronological network in the Mediterranean basin shows the potential of MR analysis to reconstruct the history of past climatic extremes and to predict future forest dynamics in a changing climate.

Between violent and non-violent action strategies: a study on extreme-right organizations in Italy and Spain. IHS Political Science Series No. 130, July 2012

This paper focuses on the different forms of action adopted by extreme right organizations (both political parties and non-party groups) in Italy and Spain during their recent mobilization and links them to the environmental conditions and internal organizational factors which might affect them. With particular attention paid to the actors’ perceptions of reality, the macro-level factors (such as the favourable or unfavourable political opportunities of the context, the availability of allies in power, the degree of repression by authorities, etc.) as well as the meso-level factors (such as the internal characteristics of extreme right groups and their dynamics) will be explored in order to understand the action strategies of extreme right organizations and their recourse to violence. This paper, drawing on a combination of qualitative and quantitative research techniques, will be based on 20 semi-structured interviews with extreme right representatives of the main right wing organizations in Italy and Spain as well as a protest event analysis of newspapers dating from 2005 to 2009.

The other side of protest music: the extreme-right and skinhead culture in democratic Portugal (1974-2015)

Although Portugal does not have a significant radical right presence in its party system, in the last decades the country did witness the development of a neo-Nazi skinhead movement that expresses its white nationalist nature and goals through the musical genres of Rock Against Communism (RAC) and the related Oi!. Utilizing various historical sources and theoretical analysis, this study contextualizes the development of nationalist music in Portugal, both before and especially during the democratic period (1974-2015). It focuses on its protagonists, domestic and international networks, as well as on the few attempts to establish a common cause with radical right-wing political parties at the turn of the century and in present times.

The effect of extreme cold temperatures on the risk of death in the two major Portuguese cities

It is well known that meteorological conditions influence the comfort and human health. Southern European countries, including Portugal, show the highest mortality rates during winter, but the effects of extreme cold temperatures in Portugal have never been estimated. The objective of this study was the estimation of the effect of extreme cold temperatures on the risk of death in Lisbon and Oporto, aiming the production of scientific evidence for the development of a real-time health warning system. Poisson regression models combined with distributed lag non-linear models were applied to assess the exposure-response relation and lag patterns of the association between minimum temperature and all-causes mortality and between minimum temperature and circulatory and respiratory system diseases mortality from 1992 to 2012, stratified by age, for the period from November to March. The analysis was adjusted for over dispersion and population size, for the confounding effect of influenza epidemics and controlled for long-term trend, seasonality and day of the week. Results showed that the effect of cold temperatures in mortality was not immediate, presenting a 1–2-day delay, reaching maximumincreased risk of death after 6–7 days and lasting up to 20–28 days. The overall effect was generally higher and more persistent in Lisbon than in Oporto, particularly for circulatory and respiratory mortality and for the elderly. Exposure to cold temperatures is an important public health problem for a relevant part of the Portuguese population, in particular in Lisbon.

Climate change in mountain regions: how local communities adapt to extreme events

This paper examines how local communities adapt to climate change and how governance structures can foster or undermine adaptive capacity. Climate change policies, in general, and disaster risk management in mountain regions, in particular, are characterised by their multi-level and multi-sectoral nature during formulation and implementation. The involvement of numerous state and non-state actors at local to national levels produces a variety of networks of interaction and communication. The paper argues that the structure of these relational patterns is critical for understanding adaptive capacity. It thus proposes an expanded concept of adaptive capacity that incorporates (horizontal and vertical) actor integration and communication flow between these actors. The paper further advocates the use of formal social network analysis to assess these relational patterns. Preliminary results from research on adaptation to climate change in a Swiss mountain region vulnerable to floods and other natural hazards illustrate the conceptual and empirical significance of the main arguments.

Genetic and environmental influences on extreme personality dispositions in adolescent female twins

Background: The objective was to determine whether the pattern of environmental and genetic influences on deviant personality scores differs from that observed for the normative range of personality, comparing results in adolescent and adult female twins. Methods: A sample of 2,796 female adolescent twins ascertained from birth records provided Junior Eysenck Personality Questionnaire data. The average age of the sample was 17.0 years ( S. D. 2.3). Genetic analyses of continuous and extreme personality scores were conducted. Results were compared for 3,178 adult female twins. Results: Genetic analysis of continuous traits in adolescent female twins were similar to findings in adult female twins, with genetic influences accounting for between 37% and 44% of the variance in Extraversion (Ex), Neuroticism (N), and Social Non-Conformity (SNC), with significant evidence of shared environmental influences (19%) found only for SNC in the adult female twins. Analyses of extreme personality characteristics, defined categorically, in the adolescent data and replicated in the adult female data, yielded estimates for high N and high SNC that deviated substantially (p < .05) from those obtained in the continuous trait analyses, and provided suggestive evidence that shared family environment may play a more important role in determining personality deviance than has been previously found when personality is viewed continuously. However, multiple-threshold models that assumed the same genetic and environmental determinants of both normative range variation and extreme scores gave acceptable fits for each personality dimension. Conclusions: The hypothesis of differences in genetic or environmental factors responsible for N and SNC among female twins with scores in the extreme versus normative ranges was partially supported, but not for Ex.