Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story.

The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations.

Riparian woodland encroachment following flow regulation: a comparative study of Boreal and Mediterranean streams

Water development accompanying mankind development has turned rivers into endangered ecosystems. Improving the understanding of ecological responses to river management actions is a key issue for assuring sustainable water management. However, few studies have been published where ecological metrics have been quantified in response to various degrees of flow alteration. In this work, changes in natural distribution of trees and shrubs within the riparian corridor (as indicator of the ecological status of the fluvial ecosystem) were quantified at multiple sites along a flow alteration gradient (as indicator of impact) along two regulated river reaches, one Boreal and the other Mediterranean, each downstream of a dam. Based on the obtained relationships we evaluated differences in response trends related to local physico-climatic factors of the two biomes and regarding to differing life-forms. Woody vegetation establishment patterns represented objective indicators of ecological responses to flow alteration. We found different responses between life-forms. Both trees and shrubs migrated downwards to the channel after dam closure, but shrubs were most impacted under higher degrees of flow alteration in terms of lateral movement. In addition, our results show clear longitudinal recovery trends of natural patterns of tree and shrub distribution corresponding to a decrease in intensity of hydrologic alteration in the Boreal river. However, vegetation encroachment persisted along the entire Mediterranean study reach. This may result from a relatively low gradient of decrease of hydrologic alteration with distance from the dam, coupled with other overlapping pressures and the mediating effect of physico-climatic characteristics on vegetation responses.

A large strain anisotropic elastoplastic continuum theory for nonlinear kinematic hardening and texture evolution

In this paper we present a continuum theory for large strain anisotropic elastoplasticity based on a decomposition of the modified plastic velocity gradient into energetic and dissipative parts. The theory includes the Armstrong and Frederick hardening rule as well as multilayer models as special cases even for large strain anisotropic elastoplasticity. Texture evolution may also be modelled by the formulation, which allows for a meaningful interpretation of the terms of the dissipation equation

Numerical issues in Lagrangian tracking and topological evolution of fluid particles in wallbounded turbulent flows

The determination of the local Lagrangian evolution of the flow topology in wall-bounded turbulence, and of the Lagrangian evolution associated with entrainment across the turbulent / non-turbulent interface into a turbulent boundary layer, require accurate tracking of a fluid particle and its local velocity gradients. This paper addresses the implementation of fluid-particle tracking in both a turbulent boundary layer direct numerical simulation and in a fully developed channel flow simulation. Determination of the sub-grid particle velocity is performed using both cubic B-spline, four-point Hermite spline and higher-order Hermite spline interpolation. Both wall-bounded flows show similar oscillations in the Lagrangian tracers of both velocity and velocity gradients, corresponding to the movement of particles across the boundaries of computational cells. While these oscillation in the particle velocity are relatively small and have negligible effect on the particle trajectories for time-steps of the order of CFL = 0.1, they appear to be the cause of significant oscillations in the evolution of the invariants of the velocity gradient tensor.

Agile Construction and Evolution of Product-Line Architectures

Software Product Line Engineering (SPLE) has proved to have significant advantages in family-based software development, but also implies the up¬front design of a product-line architecture (PLA) from which individual product applications can be engineered. The big upfront design associated with PLAs is in conflict with the current need of "being open to change". However, the turbulence of the current business climate makes change inevitable in order to stay competitive, and requires PLAs to be open to change even late in the development. The trend of "being open to change" is manifested in the Agile Software Development (ASD) paradigm, but it is spreading to the domain of SPLE. To reduce the big upfront design of PLAs as currently practiced in SPLE, new paradigms are being created, one being Agile Product Line Engineering (APLE). APLE aims to make the development of product-lines more flexible and adaptable to changes as promoted in ASD. To put APLE into practice it is necessary to make mechanisms available to assist and guide the agile construction and evolution of PLAs while complying with the "be open to change" agile principle. This thesis defines a process for "the agile construction and evolution of product-line architectures", which we refer to as Agile Product-Line Archi-tecting (APLA). The APLA process provides agile architects with a set of models for describing, documenting and tracing PLAs, as well as an algorithm to analyze change impact. Both the models and the change impact analysis offer the following capabilities: Flexibility & adaptability at the time of defining software architectures, enabling change during the incremental and iterative design of PLAs (anticipated or planned changes) and their evolution (unanticipated or unforeseen changes). Assistance in checking architectural integrity through change impact analysis in terms of architectural concerns, such as dependencies on earlier design decisions, rationale, constraints, and risks, etc.Guidance in the change decision-making process through change im¬pact analysis in terms of architectural components and connections. Therefore, APLA provides the mechanisms required to construct and evolve PLAs that can easily be refined iteration after iteration during the APLE development process. These mechanisms are provided in a modeling frame¬work called FPLA. The contributions of this thesis have been validated through the conduction of a project regarding a metering management system in electrical power networks. This case study took place in an i-smart software factory and was in collaboration with the Technical University of Madrid and Indra Software Labs. La Ingeniería de Líneas de Producto Software (Software Product Line Engi¬neering, SPLE) ha demostrado tener ventajas significativas en el desarrollo de software basado en familias de productos. SPLE es un paradigma que se basa en la reutilización sistemática de un conjunto de características comunes que comparten los productos de un mismo dominio o familia, y la personalización masiva a través de una variabilidad bien definida que diferencia unos productos de otros. Este tipo de desarrollo requiere el diseño inicial de una arquitectura de línea de productos (Product-Line Architecture, PLA) a partir de la cual los productos individuales de la familia son diseñados e implementados. La inversión inicial que hay que realizar en el diseño de PLAs entra en conflicto con la necesidad actual de estar continuamente "abierto al cam¬bio", siendo este cambio cada vez más frecuente y radical en la industria software. Para ser competitivos es inevitable adaptarse al cambio, incluso en las últimas etapas del desarrollo de productos software. Esta tendencia se manifiesta de forma especial en el paradigma de Desarrollo Ágil de Software (Agile Software Development, ASD) y se está extendiendo también al ámbito de SPLE. Con el objetivo de reducir la inversión inicial en el diseño de PLAs en la manera en que se plantea en SPLE, en los último años han surgido nuevos enfoques como la Ingeniera de Líneas de Producto Software Ágiles (Agile Product Line Engineering, APLE). APLE propone el desarrollo de líneas de producto de forma más flexible y adaptable a los cambios, iterativa e incremental. Para ello, es necesario disponer de mecanismos que ayuden y guíen a los arquitectos de líneas de producto en el diseño y evolución ágil de PLAs, mientras se cumple con el principio ágil de estar abierto al cambio. Esta tesis define un proceso para la "construcción y evolución ágil de las arquitecturas de lineas de producto software". A este proceso se le ha denominado Agile Product-Line Architecting (APLA). El proceso APLA proporciona a los arquitectos software un conjunto de modelos para de¬scribir, documentar y trazar PLAs, así como un algoritmo para analizar vel impacto del cambio. Los modelos y el análisis del impacto del cambio ofrecen: Flexibilidad y adaptabilidad a la hora de definir las arquitecturas software, facilitando el cambio durante el diseño incremental e iterativo de PLAs (cambios esperados o previstos) y su evolución (cambios no previstos). Asistencia en la verificación de la integridad arquitectónica mediante el análisis de impacto de los cambios en términos de dependencias entre decisiones de diseño, justificación de las decisiones de diseño, limitaciones, riesgos, etc. Orientación en la toma de decisiones derivadas del cambio mediante el análisis de impacto de los cambios en términos de componentes y conexiones. De esta manera, APLA se presenta como una solución para la construcción y evolución de PLAs de forma que puedan ser fácilmente refinadas iteración tras iteración de un ciclo de vida de líneas de producto ágiles. Dicha solución se ha implementado en una herramienta llamada FPLA (Flexible Product-Line Architecture) y ha sido validada mediante su aplicación en un proyecto de desarrollo de un sistema de gestión de medición en redes de energía eléctrica. Dicho proyecto ha sido desarrollado en una fábrica de software global en colaboración con la Universidad Politécnica de Madrid e Indra Software Labs.

Meteocean Influence on Inland and Coastal Floods in the East of Spain

The Santa Irene flood, at the end of October 1982, is one of the most dramatically and widely reported flood events in Spain. Its renown is mainly attributable to the collapse of the Tous dam, but its main message is to be the paradigm of the incidence of the maritime/littoral weather and its temporal sea-level rise on the coastal plains inland floods. The Santa Irene flood was attributable to a meteorological phenomenon known as gota fría (cold drop), a relatively frequent and intense rainy phenomenon on the Iberian Peninsula, particularly on the Spanish E to SE inlands and coasts. There are some circumstances that can easily come together to unleash the cold drop there: cold and dry polar air masses coming onto the whole Iberian Peninsula and the north of Africa, high sea-water temperatures, and low atmospheric pressure (cyclone) areas in the western Mediterranean basin; these circumstances are quite common during the autumn and, as it happens, in other places around the world (E/SE Africa). Their occurrence, however, shows a great space-temporal variability (in a similar way to hurricanes on Caribbean and western North Atlantic areas or also in a similar way to typhoons). In fact, all of these are equivalent, although different, phenomena, able to have a different magnitude each time. This paper describes the results of a detailed analysis and reflection about this cold drop phenomenon as a whole, on the generation of its rains, and on the different natures and consequences of its flood. This paper also explains the ways in which the nearby maritime weather and the consequential sea level govern floods on different zones of any hydrographical basin. The Santa Irene case can be considered as a paradigm to explain the influence of nearby maritime climatic conditions on flooding phenomena not only in coastal but also in upward inland areas.

Decomposition driven interface evolution for layers of binary mixtures: I. Model dirivation and base states

A dynamical model is proposed to describe the coupled decomposition and profile evolution of a free surfacefilm of a binary mixture. An example is a thin film of a polymer blend on a solid substrate undergoing simultaneous phase separation and dewetting. The model is based on model-H describing the coupled transport of the mass of one component (convective Cahn-Hilliard equation) and momentum (Navier-Stokes-Korteweg equations) supplemented by appropriate boundary conditions at the solid substrate and the free surface. General transport equations are derived using phenomenological nonequilibrium thermodynamics for a general nonisothermal setting taking into account Soret and Dufour effects and interfacial viscosity for the internal diffuse interface between the two components. Focusing on an isothermal setting the resulting model is compared to literature results and its base states corresponding to homogeneous or vertically stratified flat layers are analyzed.

Similarities and Differences in Barrel Vaults of Traditional and Stately Houses in the Historic Centre of Arequipa, Perú

The traditional architecture of the centre of the city of Arequipa has been analyzed by comparing floor-plans of houses from the eighteenth and nineteenth centuries in order to explain the reasons behind the arrangement of their constructional elements and the evolution of said elements and floor-plans. The historic centre of Arequipa, a city located in the South of Perú, South America (Latitude 16°23' South, Longitude 71 °31' West), is based on a ground plan from 1540 that was set during the city's Spanish foundation. It was declared Patrimony of the Humanity by UNESCO. The manorial architecture is widely known for its decorated fronts and one-of-a-kind designs, but its differences with respect to the popular architecture are not based exclusively on decorative aspects. Peru's colonial period finished around 1825, but the barrel-vault, construction style continued in Arequipa through 1868, when an earthquake destroyed the city. Thereafter, the vaults were replaced by roofs made of rails, with cinders made out of the lava stone. The stately houses belonged to the founding families who settled around the main square on forty nine blocks that formed a square-grid, street layout. Also belonging to this category are the houses of landlords and traders from post-colonial times.

Analysis of duplication in the Spanish durum wheat collection maintained in the CRF-INIA on the basis of agro-morphological traits and gliadin proteins

A total of 106 potential duplicate cases involved 277 accessions were detected on the basis of passport data in the durum wheat collection maintained in the CRF-INIA. Similarity between accessions was measured by agro-morphological traits. The 90% of the agro-morphological duplication were verified with gliadin proteins, allowing identification of similar material with greater refinement than agro-morphological data. However, the results indicated not to decide for rationalisation only on the basis of molecular data.