Combining a Similar Coefficient Identification Algorithm with the Boundary Element Method

The boundary element method (BEM) has been applied successfully to many engineering problems during the last decades. Compared with domain type methods like the finite element method (FEM) or the finite difference method (FDM) the BEM can handle problems where the medium extends to infinity much easier than domain type methods as there is no need to develop special boundary conditions (quiet or absorbing boundaries) or infinite elements at the boundaries introduced to limit the domain studied. The determination of the dynamic stiffness of arbitrarily shaped footings is just one of these fields where the BEM has been the method of choice, especially in the 1980s. With the continuous development of computer technology and the available hardware equipment the size of the problems under study grew and, as the flop count for solving the resulting linear system of equations grows with the third power of the number of equations, there was a need for the development of iterative methods with better performance. In [1] the GMRES algorithm was presented which is now widely used for implementations of the collocation BEM. While the FEM results in sparsely populated coefficient matrices, the BEM leads, in general, to fully or densely populated ones, depending on the number of subregions, posing a serious memory problem even for todays computers. If the geometry of the problem permits the surface of the domain to be meshed with equally shaped elements a lot of the resulting coefficients will be calculated and stored repeatedly. The present paper shows how these unnecessary operations can be avoided reducing the calculation time as well as the storage requirement. To this end a similar coefficient identification algorithm (SCIA), has been developed and implemented in a program written in Fortran 90. The vertical dynamic stiffness of a single pile in layered soil has been chosen to test the performance of the implementation. The results obtained with the 3-d model may be compared with those obtained with an axisymmetric formulation which are considered to be the reference values as the mesh quality is much better. The entire 3D model comprises more than 35000 dofs being a soil region with 21168 dofs the biggest single region. Note that the memory necessary to store all coefficients of this single region is about 6.8 GB, an amount which is usually not available with personal computers. In the problem under study the interface zone between the two adjacent soil regions as well as the surface of the top layer may be meshed with equally sized elements. In this case the application of the SCIA leads to an important reduction in memory requirements. The maximum memory used during the calculation has been reduced to 1.2 GB. The application of the SCIA thus permits problems to be solved on personal computers which otherwise would require much more powerful hardware.

Comparison of NDVI fields obtained from different remote sensors

Satellite image data have become an important source of information for monitoring vegetation and mapping land cover at several scales. Beside this, the distribution and phenology of vegetation is largely associated with climate, terrain characteristics and human activity. Various vegetation indices have been developed for qualitative and quantitative assessment of vegetation using remote spectral measurements. In particular, sensors with spectral bands in the red (RED) and near-infrared (NIR) lend themselves well to vegetation monitoring and based on them [(NIR - RED) / (NIR + RED)] Normalized Difference Vegetation Index (NDVI) has been widespread used. Given that the characteristics of spectral bands in RED and NIR vary distinctly from sensor to sensor, NDVI values based on data from different instruments will not be directly comparable. The spatial resolution also varies significantly between sensors, as well as within a given scene in the case of wide-angle and oblique sensors. As a result, NDVI values will vary according to combinations of the heterogeneity and scale of terrestrial surfaces and pixel footprint sizes. Therefore, the question arises as to the impact of differences in spectral and spatial resolutions on vegetation indices like the NDVI and their interpretation as a drought index. During 2012 three locations (at Salamanca, Granada and Córdoba) were selected and a periodic pasture monitoring and botanic composition were achieved. Daily precipitation, temperature and monthly soil water content were measurement as well as fresh and dry pasture weight. At the same time, remote sensing images were capture by DEIMOS-1 and MODIS of the chosen places. DEIMOS-1 is based on the concept Microsat-100 from Surrey. It is conceived for obtaining Earth images with a good enough resolution to study the terrestrial vegetation cover (20x20 m), although with a great range of visual field (600 km) in order to obtain those images with high temporal resolution and at a reduced cost. By contranst, MODIS images present a much lower spatial resolution (500x500 m). The aim of this study is to establish a comparison between two different sensors in their NDVI values at different spatial resolutions. Acknowledgements. This work was partially supported by ENESA under project P10 0220C-823. Funding provided by Spanish Ministerio de Ciencia e Innovación (MICINN) through project no. MTM2009-14621 and i-MATH No. CSD2006-00032 is greatly appreciated.

Fibras ópticas: interacción dispersion-chirp en sistemas ópticos modulados directamente

En los sistemas de comunicación por fibra óptica, la configuración usualmente empleada para velocidades de transmisión no superiores a 10 Gb/s es la modulación directa del láser (DML). Esta configuración presenta diversas ventajas frente a la modulación externa, como son un bajo coste, simplicidad de diseño, tamaño reducido y una elevada potencia de emisión. Sin embargo, el desplazamiento de la frecuencia nominal del láser (chirp) asociado al DML es un grave inconveniente al que deben enfrentarse los sistemas que trabajan con este modelo de transmisor. En este trabajo se propone un método para la optimización de los sistemas modulados directamente. Este método determina bajo qué condiciones se consigue contrarrestar la dispersión acumulada en el enlace ajustando adecuadamente el chirp del láser y los fenómenos no lineales que se generan en la fibra óptica.

Comunicaciones Ópticas de Banda Ancha con Fase Modulada: "Estudio de la Degradación de la Señal Óptica"

En el presente proyecto final de carrera se lleva a cabo un estudio de los sistemas de comunicaciones ópticas de 100 Gb/s. En la primera parte del proyecto se repasan las principales técnicas de modulación y de recepción de la portadora óptica, se presentan los diferentes formatos avanzados de modulación digital empleados para transmisiones de banda ancha y se discute por qué las modulaciones QPSK y DQPSK ofrecen mejores prestaciones que el resto a 100 Gb/s. La segunda parte compone el grueso del proyecto. Se centra en el estudio y la optimización de los sistemas ópticos de 100 Gb/s que hacen uso de los formatos de fase en cuadratura anteriores. De dicho análisis se pretende conocer cómo se degradan este tipo de señales a medida que se propagan por la fibra a estas velocidades. Intentaremos descubrir además cómo controlar ciertos parámetros de diseño como el ciclo de trabajo de la portadora óptica, el mapa de dispersión del enlace, la potencia inyectada a la fibra, la longitud de los vanos de amplificación …, para conseguir reducir la penalización sufrida por las limitaciones anteriores. La detección óptica coherente, la multiplexación en polarización, fibras de gran área efectiva y elevado coeficiente de dispersión cromática, unidas al uso de los formatos de fase en cuadratura, componen la mejor solución tecnológica para conseguir hacer realidad las transmisiones ópticas a 100 Gb/s de larga y ultra-larga distancia. Con el objetivo de completar el estudio teórico anterior, se diseñará una red óptica de banda ancha sobre la que se aplicarán las técnicas de diseño desarrolladas a lo largo del proyecto.

High data rate modulation of high power 1060-nm DBR tapered lasers with separate contacts

Direct optical modulation at 2.5 Gb/s with amplitude of more than 0.5 W has been demonstrated in single longitudinal mode distributed Bragg reflector tapered lasers emitting at 1060 nm with separated injection of the ridge waveguide and tapered sections. The modulating signal of ~110 mA peak to peak was applied to the ridge waveguide section, yielding a high modulation efficiency of ~5 W/A. The large-signal frequency response of the experimental set-up was limited by the bandwidth of the electrical amplifier rather than by the internal dynamics of the laser, indicating that higher bit rates could be achieved with improved driving electronics.

Comunicaciones Ópticas de Banda Ancha con Fase Modulada: "Estudio de la Degradación de la Señal Óptica"

En el presente proyecto final de carrera se lleva a cabo un estudio de los sistemas de comunicaciones ópticas de 100 Gb/s. En la primera parte del proyecto se repasan las principales técnicas de modulación y de recepción de la portadora óptica, se presentan los diferentes formatos avanzados de modulación digital empleados para transmisiones de banda ancha y se discute por qué las modulaciones QPSK y DQPSK ofrecen mejores prestaciones que el resto a 100 Gb/s. La segunda parte compone el grueso del proyecto. Se centra en el estudio y la optimización de los sistemas ópticos de 100 Gb/s que hacen uso de los formatos de fase en cuadratura anteriores. De dicho análisis se pretende conocer cómo se degradan este tipo de señales a medida que se propagan por la fibra a estas velocidades. Intentaremos descubrir además cómo controlar ciertos parámetros de diseño como el ciclo de trabajo de la portadora óptica, el mapa de dispersión del enlace, la potencia inyectada a la fibra, la longitud de los vanos de amplificación …, para conseguir reducir la penalización sufrida por las limitaciones anteriores. La detección óptica coherente, la multiplexación en polarización, fibras de gran área efectiva y elevado coeficiente de dispersión cromática, unidas al uso de los formatos de fase en cuadratura, componen la mejor solución tecnológica para conseguir hacer realidad las transmisiones ópticas a 100 Gb/s de larga y ultra-larga distancia. Con el objetivo de completar el estudio teórico anterior, se diseñará una red óptica de banda ancha sobre la que se aplicarán las técnicas de diseño desarrolladas a lo largo del proyecto.

Modelo Híbrido para la Ayuda al Capitán

En esta Tesis se plantea una nueva forma de entender la evacuación apoyándonos en tecnologías existentes y accesibles que nos permitirán ver este proceso como un ente dinámico. Se trata de una metodología que implica no solo el uso de herramientas de análisis que permitan la definición de planes de evacuación en tiempo real, sino que también se apunta hacia la creación de una infraestructura física que permita alimentar con información actualizada al sistema de forma que, según la situación y la evolución de la emergencia, sea posible realizar planes alternativos que se adapten a las nuevas circunstancias. En base a esto, el sistema asimilará toda esa información y aportará soluciones que faciliten la toma de decisiones durante toda la evolución del incidente. Las aportaciones originales de esta Tesis son múltiples y muy variadas, pudiéndolas resumir en los siguientes puntos: 1. Estudio completo del estado del arte: a. Detección y análisis de diferentes proyectos a nivel internacional que de forma parcial tratan algunos aspectos desarrollados en la Tesis. b. Completo estudio a nivel mundial del software desarrollado total o parcialmente para la simulación del comportamiento humano y análisis de procesos de evacuación. Se ha generado una base de datos que cataloga de forma exhaustiva estas aplicaciones, permitiendo realizar un completo análisis y posibilitando la evolución futura de los contenidos de la misma. En la tesis se han analizado casi un centenar de desarrollos, pero el objetivo es seguir completando esta base de datos debido a la gran utilidad y a las importantes posibilidades que ofrece. 2. Desarrollo de un importante capítulo que trata sobre la posibilidad de utilizar entornos virtuales como alternativa intermedia al uso de simuladores y simulacros. En esta sección se divide en dos bloques: a. Ensayos en entornos reales y virtuales. b. Ensayos en entornos virtuales (pruebas realizadas con varios entornos virtuales). 3. Desarrollo de e-Flow net design: paquete de herramientas desarrolladas sobre Rhinoceros para el diseño de la red de evacuación basada en los elementos definidos en la tesis: Nodes, paths, Relations y Areas. 4. Desarrollo de e-Flow Simulator: Conjunto de herramientas que transforman Rhinoceros en un simulador 3D de comportamiento humano. Este simulador, de desarrollo propio, incorpora un novedoso algoritmo de comportamiento a nivel de individuo que incluye aspectos que no se han encontrado en otros simuladores. Esta herramienta permite realizar simulaciones programadas de grupos de individuos cuyo comportamiento se basa en el análisis del entorno y en la presencia de referencias dinámicas. Incluye otras importantes novedades como por ejemplo: herramientas para análisis de la señalización, elementos de señalización dinámica, incorporación sencilla de obstáculos, etc. También se ha creado una herramienta que posibilita la implementación del movimiento del propio escenario simulando la oscilación del mismo, con objeto de reflejar la influencia del movimiento del buque en el desplazamiento de los individuos. 5. En una fase avanzada del desarrollo, se incorporó la posibilidad de generar un vídeo de toda la simulación, momento a partir del cual, se han documentado todas las pruebas (y se continúan documentando) en una base de datos que recoge todas las características de las simulaciones, los problemas detectados, etc. Estas pruebas constituyen, en el momento en que se ha cerrado la redacción de la Tesis, un total de 81 GB de datos. Generación y análisis de rutas en base a la red de evacuación creada con e-Flow Net design y las simulaciones realizadas con e-Flow Net simulator. a. Análisis para la optimización de la configuración de la red en base a los nodos por área existentes. b. Definición de procesos previos al cálculo de rutas posibles. c. Cálculo de rutas: i. Análisis de los diferentes algoritmos que existen en la actualidad para la optimización de rutas. ii. Desarrollo de una nueva familia de algoritmos que he denominado “Minimum Decision Algorithm (MDA)”, siendo los algoritmos que componen esta familia: 1. MDA básico. 2. MDA mínimo. 3. MDA de no interferencia espacial. 4. MDA de expansión. 5. MDA de expansión ordenada para un único origen. 6. MDA de expansión ordenada. iii. Todos estos algoritmos se han implementado en la aplicación e-Flow creada en la Tesis para el análisis de rutas y que constituye el núcleo del Sistema de Ayuda al Capitán. d. Determinación de las alternativas para el plan de evacuación. Tras la definición de las rutas posibles, se describen diferentes procesos existentes de análisis por ponderación en base a criterios, para pasar finalmente a definir el método de desarrollo propio propuesto en esta Tesis y cuyo objetivo es responder en base a la población de rutas posibles obtenidas mediante los algoritmos MDA, qué combinación de rutas constituyen el Plan o Planes más adecuados para cada situación. La metodología creada para la selección de combinaciones de rutas que determinan un Plan completo, se basa en cuatro criterios básicos que tras su aplicación ofrecen las mejores alternativas. En esta fase también se incluye un complejo análisis de evolución temporal que incorpora novedosas definiciones y formulaciones. e. Derivado de la definición de la metodología creada en esta Tesis para la realización de los análisis de evolución temporal, se ha podido definir un nuevo teorema matemático que se ha bautizado como “Familia de cuadriláteros de área constante”. 7. Especificación de la infraestructura física del Sistema de Ayuda al Capitán: parte fundamental de sistema es la infraestructura física sobre la que se sustentaría. Esta infraestructura estaría compuesta por sensores, actuadores, aplicaciones para dispositivos móviles, etc. En este capítulo se analizan los diferentes elementos que la constituirían y las tecnologías implicadas. 8. Especificación de la infraestructura de servicios. 9. Creación del Blog Virtual Environments (http://epcinnova-virtualenvironments.blogspot.com.es/) en el que se han publicado todas las pruebas realizadas en el capítulo que analiza los entornos virtuales como alternativa a los simuladores y a los ensayos en laboratorio o los simulacros, incluyendo en muchos casos la posibilidad de que el visitante del blog pueda realizar la simulación en el entorno virtual. Este blog también incluye otras secciones que se han trabajado durante la Tesis: • Recopilación de diferentes entornos virtuales existentes. • Diagrama que recopila información sobre accidentes tanto en el ámbito marítimo como en el terrestre (en desarrollo). • Esquema propuesto para el acopio de información obtenida a partir de un simulacro. 10. Esta Tesis es la base para el proyecto e-Flow (nombre de una de las aplicaciones que desarrolladas en esta obra), un proyecto en el que el autor de esta Tesis ha trabajado como Project Manager. En el proyecto participa un consorcio de empresas y la UPM, y tiene como objetivo trasladar a la realidad gran parte de los planteamientos e ideas presentadas en esta Tesis. Este proyecto incluye el desarrollo de la infraestructura física y de servicios que permitirán, entre otras cosas, implementar en infraestructuras complejas una plataforma que posibilita la evacuación dinámica y un control ubicuo de los sistemas de monitorización y actuación implementados. En estos momentos se está finalizando el proyecto, cuyo objetivo final es la implementación de un piloto en un Hospital. También destacamos los siguientes avances a nivel de difusión científico-tecnológico: • Ponencia en el “52 congreso de la Ingeniería Naval en España” presentando un artículo “e-Flow- Sistema integral inteligente de soporte a la evacuación”. En este artículo se trata tanto el proyecto e-Flow del que soy Project Manager, como esta Tesis Doctoral, al ser temas estrechamente vinculados. En 2014 se publicó en dos números de la Revista Ingeniería Naval el artículo presentado a estas jornadas. • Co-autor en el artículo “E-Flow: A communication system for user notification in dynamic evacuation scenarios” presentado en el 7th International Conference on Ubicuous Computing & Ambient Intelligence (UCAMI) celebrado en Costa Rica. Por último, una de las aportaciones más interesantes, es la definición de un gran número de líneas de investigación futuras en base a todos los avances realizados en esta Tesis. ABSTRACT With this Thesis a new approach for understanding evacuation process is considered, taking advantage of the existing and open technologies that will allow this process to be interpreted as a dynamic entity. The methodology involves not only tools that allows on.-time evacuation plans, but also creates a physical insfrastructure that makes possible to feed the system with information on real time so, considering in each moment the real situation as well as the specific emergency development it will be feasible to generate alternative plans that responds to the current emergency situation. In this respect, the system will store all this information and will feedback with solutions that will help the decision making along the evacuation process. The innovative and singular contributions of this Thesis are numerous and rich, summarised as follows: 1.- Complete state-of-art study: a. Detection and analysis of different projects on an international level that, although partially, deal with some aspects developed in this Thesis. b. Thorough study at a international level of the developed software - total or partially done - for the simulation of the human behaviour and evacuation processes analysis. A database has been generated that classifies in detail these applications allowing to perform a full analysis and leading to future evolution of its contents. Within the Thesis work, almost a hundred of developments have been analysed but the purpose is to keep up updating this database due to the broad applications and possibilities that it involves. 2. Development of an important chapter that studies the possibility of using virtual scenarios as mid-term alternative for the use of simulations. This section is divided in two blocks: a. Trials in virtual and real scenarios b. Trials in virutal scenarios (trials performed with several ones). 3. E-Flow net design development: Set of tools developed under Rhinoceros for the evacuation net design based on the elements defined in the Thesis: Nodes, Paths, Relations, Areas 4. E-Flow simulator development: Set of tools that uses Rhinoceros as a 3D simulator of human behaviour. This simulator, of my own design, includes a new and original algorithm of human behaviour that involves aspects that are not found in other simulators. This tool allows to perform groups programmed simulations which behaviour is based on their enviroment analysis and presence of dynamic references. It includes other important innovations as for example: tools for signals analysis, dynamic signal elements, easy obstacle adding etc... More over, a tool that allows the own scenario movement implementation has been created by simulating the own oscillation movement, with the purpose of playing the vessel movement's influences in the individuals' displacements. 5. In an advanced stage of the development, the possibility of generating a video recording of all the simulation was also integrated, then from that moment all tests have been filed (and keep on doing so) in a database that collects all simulation characteristics, failures detected, etc. These stored tests amounts to a total of 81 GB at the moment of finishing the Thesis work. Generation and analysis of paths regarding the evacuation net created with E-Flow design and the simulations performed with E-Flow net Simulator. a. Analysis for the optimisation of the network configuration based in the existing nodes per area. b. Definition of the processes previous to the calculation of the feasible paths c. Paths calculation: i. Analysis of the different algorithms on existance nowadays for the routes optimisation. ii. Development of a new family of algorithms that I have called “Minimum Decision Algorithm (MDA)”, being composed of: 1. MDA basic 2. MDA minimum 3. MDA of not spacial interference 4. MDA of expansion (es de extenderse) o enlargement ( es de crecimiento) 5. MDA of organised expansion for a single origin (of organised enlargement for a single origin) 6. MDA of organised expansion (of organised enlargement) iii. All these algorithms have been implemented in the E-Flow application created in the Thesis dfor the routes analysis and it is the core of the Captain's support system. d. Determination of the alternatives for the evacuation plan. After defining all possible paths, different processes of analysis existing for weighing-based criteria are described, thus to end defining the own development method proposed in this Thesis and that aims to respond in an agreggation of possible routes basis obtained by means of the MDA algorithms what is the routes' combination more suitable for the Plan or Plans in every situation. The methodology created fot the selection of the combinations of routes that determine a complete Plan is baesd in four basic criteria that after applying, offer the best alternatives. In this stage a complex analysis of the progress along time is also included, that adds original and innovative defintions and formulations. e. Originated from the methodology created in this Thesis for the perfoming of the analysy of the progress along time, a new mathematic theorem has been defined, that has been called as "Family of quadrilateral of constant area". 7. Specification of the physiscal infrastructure of the Captain's help system: essential part is this physical infrastructure that will support it. This system will be made of sensors, actuators, apps for mobile devices etc... Within this chapter the different elements and technologies that make up this infrastructure will be studied. 8. Specification for the services infrastructure. 9. Start up of the Blog. " Virtual Environments (http://epcinnova-virtualenvironments.blogspot.com.es/)" in which all tests performed have been published in terms of analysis of the virtual enviroments as alternative to the simulators as well as to the laboratory experiments or simulations, including in most of the cases the possibility that the visitor can perform the simulation within the virtual enviroment. This blog also includes other sections that have been worked along and within this Thesis: - Collection of different virtual scenarios existent. - Schema that gathers information concerning accidents for maritime and terrestrial areas (under development) - Schema proposed for the collecting of information obtained from a simulation. 10. This Thesis is the basis of the E-Flow project (name of one of the applications developed in this work), a project in which the Thesis' author has worked in as Project Manager. In the project takes part a consortium of firms as well as the UPM and the aim is to bring to real life most part of the approaches and ideas contained in this Thesis. This project includes the development of the physical infrastructure as well as the services that will allow, among others, implement in complex infrastrucutres a platform that will make possible a dynamic evacuation and a continuous control of the monitoring and acting systems implemented. At the moment the project is getting to an end which goal is the implementation of a pilot project in a Hospital. We also would like to highlight the following advances concerning the scientific-technology divulgation: • Talk in the " 52th Congress of the Naval Engineering in Spain" with the article "E-Flow . Intelligent system integrated for supporting evacuation". This paper is about project E-Flow which I am Project Manager of, as well as this Thesis for the Doctorate, being both closely related. Two papers published In 2014 in the Naval Engineering Magazine. • Co-author in the article “E-Flow: A communication system for user notification in dynamic evacuation scenarios” [17] introduced in the 7th International Conference on Ubicuous Computing & Ambient Intelligence (UCAMI) held in Costa Rica. Last, but not least, one of the more interesting contributions is the defintion of several lines of research in the future, based on the advances made in this Thesis.

Efficient parallelization of a regional ocean model for the western Mediterranean Sea

This paper focuses on the parallelization of an ocean model applying current multicore processor-based cluster architectures to an irregular computational mesh. The aim is to maximize the efficiency of the computational resources used. To make the best use of the resources offered by these architectures, this parallelization has been addressed at all the hardware levels of modern supercomputers: firstly, exploiting the internal parallelism of the CPU through vectorization; secondly, taking advantage of the multiple cores of each node using OpenMP; and finally, using the cluster nodes to distribute the computational mesh, using MPI for communication within the nodes. The speedup obtained with each parallelization technique as well as the combined overall speedup have been measured for the western Mediterranean Sea for different cluster configurations, achieving a speedup factor of 73.3 using 256 processors. The results also show the efficiency achieved in the different cluster nodes and the advantages obtained by combining OpenMP and MPI versus using only OpenMP or MPI. Finally, the scalability of the model has been analysed by examining computation and communication times as well as the communication and synchronization overhead due to parallelization.

Chromophore-assisted light inactivation and self-organization of microtubules and motors

Chromophore-assisted light inactivation (CALI) offers the only method capable of modulating specific protein activities in localized regions and at particular times. Here, we generalize CALI so that it can be applied to a wider range of tasks. Specifically, we show that CALI can work with a genetically inserted epitope tag; we investigate the effectiveness of alternative dyes, especially fluorescein, comparing them with the standard CALI dye, malachite green; and we study the relative efficiencies of pulsed and continuous-wave illumination. We then use fluorescein-labeled hemagglutinin antibody fragments, together with relatively low-power continuous-wave illumination to examine the effectiveness of CALI targeted to kinesin. We show that CALI can destroy kinesin activity in at least two ways: it can either result in the apparent loss of motor activity, or it can cause irreversible attachment of the kinesin enzyme to its microtubule substrate. Finally, we apply this implementation of CALI to an in vitro system of motor proteins and microtubules that is capable of self-organized aster formation. In this system, CALI can effectively perturb local structure formation by blocking or reducing the degree of aster formation in chosen regions of the sample, without influencing structure formation elsewhere.

Hepatitis C virus and other Flaviviridae viruses enter cells via low density lipoprotein receptor

Endocytosis of the Flaviviridae viruses, hepatitis C virus, GB virus C/hepatitis G virus, and bovine viral diarrheal virus (BVDV) was shown to be mediated by low density lipoprotein (LDL) receptors on cultured cells by several lines of evidence: by the demonstration that endocytosis of these virus correlated with LDL receptor activity, by complete inhibition of detectable endocytosis by anti-LDL receptor antibody, by inhibition with anti-apolipoprotein E and -apolipoprotein B antibodies, by chemical methods abrogating lipoprotein/LDL receptor interactions, and by inhibition with the endocytosis inhibitor phenylarsine oxide. Confirmatory evidence was provided by the lack of detectable LDL receptor on cells known to be resistant to BVDV infection. Endocytosis via the LDL receptor was shown to be mediated by complexing of the virus to very low density lipoprotein or LDL but not high density lipoprotein. Studies using LDL receptor-deficient cells or a cytolytic BVDV system indicated that the LDL receptor may be the main but not exclusive means of cell entry of these viruses. Studies on other types of viruses indicated that this mechanism may not be exclusive to Flaviviridae but may be used by viruses that associate with lipoprotein in the blood. These findings provide evidence that the family of LDL receptors may serve as viral receptors.

Increasing the quality of seismic interpretation

Euan Macrae was funded by a NERC Open CASE PhD award (NE/F013728/1) with Midland Valley Exploration Ltd. as the industry partner. We thank the 763 geoscientists for their participation, and in particular, the reference experts who gave their time freely to the project. Marian Scott (University of Glasgow, UK) is thanked for assisting with the statistical analysis. Four reviewers are thanked for their constructive comments which improved the manuscript.

Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B

Human cytomegalovirus (HCMV) infection alters the expression of many cellular genes, including IFN-stimulated genes (ISGs) [Zhu, H., Cong, J.-P., Mamtora, G., Gingeras, T. & Shenk, T. (1998) Proc. Natl. Acad. Sci. USA 95, 14470–14475]. By using high-density cDNA microarrays, we show that the HCMV-regulated gene expression profile in fibroblasts does not differ substantially from the response generated by IFN. Furthermore, we identified the specific viral component triggering this response as the envelope glycoprotein B (gB). Cells treated with gB, but not other herpesviral glycoproteins, exhibited the same transcriptional profile as HCMV-infected cells. Thus, the interaction of gB with its as yet unidentified cellular receptor is the principal mechanism by which HCMV alters cellular gene expression early during infection. These findings highlight a pioneering paradigm for the consequences of virus–receptor interactions.

Immunization with DNA vaccines encoding glycoprotein D or glycoprotein B, alone or in combination, induces protective immunity in animal models of herpes simplex virus-2 disease.

DNA vaccines expressing herpes simplex virus type 2 (HSV-2) full-length glycoprotein D (gD), or a truncated form of HSV-2 glycoprotein B (gB) were evaluated for protective efficacy in two experimental models of HSV-2 infection. Intramuscular (i.m.) injection of mice showed that each construction induced neutralizing serum antibodies and protected the mice from lethal HSV-2 infection. Dose-titration studies showed that low doses (< or = 1 microgram) of either DNA construction induced protective immunity, and that a single immunization with the gD construction was effective. The two DNAs were then tested in a low-dosage combination in guinea pigs. Immune sera from DNA-injected animals had antibodies to both gD and gB, and virus neutralizing activity. When challenged by vaginal infection with HSV-2, the DNA-immunized animals were significantly protected from primary genital disease.

Induction of cytotoxic T lymphocytes by intramuscular immunization with plasmid DNA is facilitated by bone marrow-derived cells.

Striated muscle is the predominant site of gene expression after i.m. immunization of plasmid DNA, but it is not clear if myocytes or professional antigen-presenting cells (APCs) of hematopoietic origin present the encoded antigens to class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL). To address this issue, CTL responses were assessed in mice engrafted with immune systems that were partially MHC matched with antigen-producing muscle cells. Spleen cells (sc) from immunocompetent F1 H-2bxd mice were infused into H-2b or H-2d mice carrying the severe combined immunodeficiency (scid) mutation, creating F1sc-->H-2b and F1sc-->H-2d chimeras, respectively. Immunization with DNA plasmids encoding the herpes simplex virus gB or the human immunodeficiency virus gp120 glycoproteins elicited antiviral CTL activity. F1sc-->H-2d chimeras responded to an H-2d-restricted gp120 epitope but not an H-2b restricted gB epitope, whereas F1sc-->H-2b chimeras responded to the H-2b but not the H-2d restricted epitope. This pattern of epitope recognition by the sc chimeras indicated that APCs of recipient (scid) origin were involved in initiation of CTL responses. Significantly, CTL responses against epitopes presented by the mismatched donor class I molecules were elicited if F1 bone marrow cells and sc were transferred into scid recipients before or several days to weeks after DNA immunization. Thus, bone marrow-derived APCs are sufficient for class I MHC presentation of viral antigens after i.m. immunization with plasmid DNA. Expression of plasmid DNA by these APCs is probably not a requirement for CTL priming. Instead, they appear to present proteins synthesized by other host cells.

Cloning of thermostable DNA polymerases from hyperthermophilic marine Archaea with emphasis on Thermococcus sp. 9 degrees N-7 and mutations affecting 3'-5' exonuclease activity.

Five extremely thermophilic Archaea from hydrothermal vents were isolated, and their DNA polymerases were cloned and expressed in Escherichia coli. Protein splicing elements (inteins) are present in many archaeal DNA polymerases, but only the DNA polymerase from strain GB-C contained an intein. Of the five cloned DNA polymerases, the Thermococcus sp. 9 degrees N-7 DNA polymerase was chosen for biochemical characterization. Thermococcus sp. 9 degrees N-7 DNA polymerase exhibited temperature-sensitive strand displacement activity and apparent Km values for DNA and dNTP similar to those of Thermococcus litoralis DNA polymerase. Six substitutions in the 3'-5' exonuclease motif I were constructed in an attempt to reduce the 3'-5' exonuclease activity of Thermococcus sp. 9 degrees N-7 DNA polymerase. Five mutants resulted in no detectable 3'-5' exonuclease activity, while one mutant (Glul43Asp) had <1% of wild-type activity.