DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Assessing agglomeration economies in the Yangzi River Delta, China : a bayesian spatial econometric approach

This paper estimates the elasticity of labor productivity with respect to employment density, a widely used measure of the agglomeration effect, in the Yangtze River Delta, China. A spatial Durbin model is presented that makes explicit the influences of spatial dependence and endogeneity bias in a very simple way. Results of Bayesian estimation using the data of the year 2009 indicate that the productivity is influenced by factors correlated with density rather than density itself and that spatial spillovers of these factors of agglomeration play a significant role. They are consistent with the findings of Ke (2010) and Artis, et al. (2011) that suggest the importance of taking into account spatial dependence and hitherto omitted variables.

Agglomeration and firm-level productivity : a Bayesian spatial approach

This paper estimates the impact of industrial agglomeration on firm-level productivity in Chinese manufacturing sectors. To account for spatial autocorrelation across regions, we formulate a hierarchical spatial model at the firm level and develop a Bayesian estimation algorithm. A Bayesian instrumental-variables approach is used to address endogeneity bias of agglomeration. Robust to these potential biases, we find that agglomeration of the same industry (i.e. localization) has a productivity-boosting effect, but agglomeration of urban population (i.e. urbanization) has no such effects. Additionally, the localization effects increase with educational levels of employees and the share of intermediate inputs in gross output. These results may suggest that agglomeration externalities occur through knowledge spillovers and input sharing among firms producing similar manufactures.

Road environment modeling using robust perspective analysis and recursive Bayesian segmentation

Recently, vision-based advanced driver-assistance systems (ADAS) have received a new increased interest to enhance driving safety. In particular, due to its high performance–cost ratio, mono-camera systems are arising as the main focus of this field of work. In this paper we present a novel on-board road modeling and vehicle detection system, which is a part of the result of the European I-WAY project. The system relies on a robust estimation of the perspective of the scene, which adapts to the dynamics of the vehicle and generates a stabilized rectified image of the road plane. This rectified plane is used by a recursive Bayesian classi- fier, which classifies pixels as belonging to different classes corresponding to the elements of interest of the scenario. This stage works as an intermediate layer that isolates subsequent modules since it absorbs the inherent variability of the scene. The system has been tested on-road, in different scenarios, including varied illumination and adverse weather conditions, and the results have been proved to be remarkable even for such complex scenarios.

Learning an L1-regularized Gaussian Bayesian Network in the Equivalence Class Space

Learning the structure of a graphical model from data is a common task in a wide range of practical applications. In this paper, we focus on Gaussian Bayesian networks, i.e., on continuous data and directed acyclic graphs with a joint probability density of all variables given by a Gaussian. We propose to work in an equivalence class search space, specifically using the k-greedy equivalence search algorithm. This, combined with regularization techniques to guide the structure search, can learn sparse networks close to the one that generated the data. We provide results on some synthetic networks and on modeling the gene network of the two biological pathways regulating the biosynthesis of isoprenoids for the Arabidopsis thaliana plant

IFMIF suitability for evaluation of fusion functional materials

The International FusionMaterials Irradiation Facility (IFMIF) is a future neutron source based on the D-Li stripping reaction, planned to test candidate fusionmaterials at relevant fusion irradiation conditions. During the design of IFMIF special attention was paid to the structural materials for the blanket and first wall, because they will be exposed to the most severe irradiation conditions in a fusion reactor. Also the irradiation of candidate materials for solid breeder blankets is planned in the IFMIF reference design. This paper focuses on the assessment of the suitability of IFMIF irradiation conditions for testing functionalmaterials to be used in liquid blankets and diagnostics systems, since they are been also considered within IFMIF objectives. The study has been based on the analysis and comparison of the main expected irradiation parameters in IFMIF and DEMO reactor.

Potential common radiation problems for components and diagnostics in future magnetic and inertial confinement fusion devices

This work aims at identifying commonpotentialproblems that futurefusiondevices will encounter for both magnetic and inertialconfinement approaches in order to promote joint efforts and to avoid duplication of research. Firstly, a comparison of radiation environments found in both fusion reaction chambers will be presented. Then, wall materials, optical components, cables and electronics will be discussed, pointing to possible future areas of common research. Finally, a brief discussion of experimental techniques available to simulate the radiation effect on materials is included

The role of spatial and temporal radiation deposition in inertial fusion chambers: the case of HiPER¿

The first wall armour for the reactor chamber of HiPER will have to face short energy pulses of 5 to 20 MJ mostly in the form of x-rays and charged particles at a repetition rate of 5–10 Hz. Armour material and chamber dimensions have to be chosen to avoid/minimize damage to the chamber, ensuring the proper functioning of the facility during its planned lifetime. The maximum energy fluence that the armour can withstand without risk of failure, is determined by temporal and spatial deposition of the radiation energy inside the material. In this paper, simulations on the thermal effect of the radiation–armour interaction are carried out with an increasing definition of the temporal and spatial deposition of energy to prove their influence on the final results. These calculations will lead us to present the first values of the thermo-mechanical behaviour of the tungsten armour designed for the HiPER project under a shock ignition target of 48 MJ. The results will show that only the crossing of the plasticity limit in the first few micrometres might be a threat after thousands of shots for the survivability of the armour.

Electromagnetic Instability Studies in Fusion Plasmas Edge

Este trabajo esta dedicado al estudio de las estructuras macroscópicas conocidas en la literatura como filamentos o blobs que han sido observadas de manera universal en el borde de todo tipo de dispositivos de fusión por confinamiento magnético. Estos filamentos, celdas convectivas elongadas a lo largo de las líneas de campo que surgen en el plasma fuertemente turbulento que existe en este tipo de dispositivos, parecen dominar el transporte radial de partículas y energía en la región conocida como Scrape-off Layer, en la que las líneas de campo dejan de estar cerradas y el plasma es dirigido hacia la pared sólida que forma la cámara de vacío. Aunque el comportamiento y las leyes de escala de estas estructuras son relativamente bien conocidos, no existe aún una teoría generalmente aceptada acerca del mecanismo físico responsable de su formación, que constituye una de las principales incógnitas de la teoría de transporte del borde en plasmas de fusión y una cuestión de gran importancia práctica en el desarrollo de la siguiente generación de reactores de fusión (incluyendo dispositivos como ITER y DEMO), puesto que la eficiencia del confinamiento y la cantidad de energía depositadas en la pared dependen directamente de las características del transporte en el borde. El trabajo ha sido realizado desde una perspectiva eminentemente experimental, incluyendo la observación y el análisis de este tipo de estructuras en el stellarator tipo heliotrón LHD (un dispositivo de gran tamaño, capaz de generar plasmas de características cercanas a las necesarias en un reactor de fusión) y en el stellarator tipo heliac TJ-II (un dispositivo de medio tamaño, capaz de generar plasmas relativamente más fríos pero con una accesibilidad y disponibilidad de diagnósticos mayor). En particular, en LHD se observó la generación de filamentos durante las descargas realizadas en configuración de alta _ (alta presión cinética frente a magnética) mediante una cámara visible ultrarrápida, se caracterizó su comportamiento y se investigó, mediante el análisis estadístico y la comparación con modelos teóricos, el posible papel de la Criticalidad Autoorganizada en la formación de este tipo de estructuras. En TJ-II se diseñó y construyó una cabeza de sonda capaz de medir simultáneamente las fluctuaciones electrostáticas y electromagnéticas del plasma. Gracias a este nuevo diagnóstico se pudieron realizar experimentos con el fin de determinar la presencia de corriente paralela a través de los filamentos (un parámetro de gran importancia en su modelización) y relacionar los dos tipos de fluctuaciones por primera vez en un stellarator. Así mismo, también por primera vez en este tipo de dispositivo, fue posible realizar mediciones simultáneas de los tensores viscoso y magnético (Reynolds y Maxwell) de transporte de cantidad de movimiento. ABSTRACT This work has been devoted to the study of the macroscopic structures known in the literature as filaments or blobs, which have been observed universally in the edge of all kind of magnetic confinement fusion devices. These filaments, convective cells stretching along the magnetic field lines, arise from the highly turbulent plasma present in this kind of machines and seem to dominate radial transport of particles and energy in the region known as Scrapeoff Layer, in which field lines become open and plasma is directed towards the solid wall of the vacuum vessel. Although the behavior and scale laws of these structures are relatively well known, there is no generally accepted theory about the physical mechanism involved in their formation yet, which remains one of the main unsolved questions in the fusion plasmas edge transport theory and a matter of great practical importance for the development of the next generation of fusion reactors (including ITER and DEMO), since efficiency of confinement and the energy deposition levels on the wall are directly dependent of the characteristics of edge transport. This work has been realized mainly from an experimental perspective, including the observation and analysis of this kind of structures in the heliotron stellarator LHD (a large device capable of generating reactor-relevant plasma conditions) and in the heliac stellarator TJ-II (a medium-sized device, capable of relatively colder plasmas, but with greater ease of access and diagnostics availability). In particular, in LHD, the generation of filaments during high _ discharges (with high kinetic to magnetic pressure ratio) was observed by means of an ultrafast visible camera, and the behavior of this structures was characterized. Finally, the potential role of Self-Organized Criticality in the generation of filaments was investigated. In TJ-II, a probe head capable of measuring simultaneously electrostatic and electromagnetic fluctuations in the plasma was designed and built. Thanks to this new diagnostic, experiments were carried out in order to determine the presence of parallel current through filaments (one of the most important parameters in their modelization) and to related electromagnetic (EM) and electrostatic (ES) fluctuations for the first time in an stellarator. As well, also for the first time in this kind of device, measurements of the viscous and magnetic momentum transfer tensors (Reynolds and Maxwell) were performed.

A Comparison of different Uncertainty Activation Cross-Section Data Libraries and collapsed values for different neutron spectra: ADS, FISSION and FUSION

PART I:Cross-section uncertainties under differentneutron spectra. PART II: Processing uncertainty libraries

Uncertainty assessment methodologies applied to Tritium production in fusion lithium breeding blankets

- Need of Tritium production - Neutronic objectives - The Frascati experiment - Measurements of Tritium activity

Temperature Evolution and Light Species Diffusion in Armor and Structural Material for Inertial Fusion Reactor Chambers: a Case for HiPER 4a

One of the most advance designs for HiPER fusion reactor is a spherical chamber 10 m in diameter based on dry wall concept. In this system, the first wall will have to withstand short energy pulses of 5 to 20 MJ at a repetition rate of 0.5-10 Hz mostly in form of X-rays and charged particles. To avoid melting of the inner surface, the first wall consists on a thin armor attached to the structural material. Thickness (th) and material of each layer have to be chosen to assure the proper functioning of the facility during its planned lifetime.