A multiproxy analysis of late MIS 6 to early MIS 5d OSP Site 161-975 sediments

A multiproxy analysis based on planktic foraminiferal abundances, derived SSTs, and stable planktic isotopes measurements together with alkenone abundances and Uk'37 SSTs was performed on late MIS 6 to early MIS 5d sediment recovered from Site 975 (ODP Leg 161) in the South Balearic Islands basin (Western Mediterranean) with emphasis on reconstructing the climate progression of the last interglacial period. A number of abrupt climate changes related to alternative influence of nutrient rich northern and oligotrophic southern water masses were revealed. Heinrich event 11 and cooling events C27, C26, C25, C24, C23, which have been previously described in the North Atlantic, were recognized. However, in comparison to the eastern North Atlantic mid-latitude region, events C27 and C26 at Site 975 seem to be significantly more pronounced. Together with evidence of a two-phase climate optimum with maximum SSTs reached during its later phase, this implies a close similarity in climate dynamics between the Western Mediterranean and the Nordic seas. We propose that postglacial effects in the Nordic seas had an influence on the western Mediterranean climate via atmospheric circulation and that these effects competed with the insolation force.

Cyber-networks, physical coalitions and missing links : imagining and realizing dissent in Malaysia 1998-2008

From September 1998 to March 2008, dissident cyber-networks in Malaysia developed connections with physical coalitions that contributed to the Opposition’s historic gains in the 12th General Election of March 2008. To succeed in entrenching a ‘two-coalition system’, however, the component parties of the Opposition coalition (Pakatan Rakyat) must establish its ‘missing links’, namely, extensive and deep organizational networks in society that would permit the coalition to move from imagining and realizing dissent to institutionalizing it meaningfully.

Arabidopsis thaliana DOF6 negatively affects germination in non-after ripened seeds and interacts with TCP14

Seed dormancy prevents seeds from germinating under environmental conditions unfavourable for plant growth and development and constitutes an evolutionary advantage. Dry storage, also known as after-ripening, gradually decreases seed dormancy by mechanisms not well understood. An Arabidopsis thaliana DOF transcription factor gene (DOF6) affecting seed germination has been characterized. The transcript levels of this gene accumulate in dry seeds and decay gradually during after-ripening and also upon seed imbibition. While constitutive over-expression of DOF6 produced aberrant growth and sterility in the plant, its over-expression induced upon seed imbibition triggered delayed germination, abscisic acid (ABA)-hypersensitive phenotypes and increased expression of the ABA biosynthetic gene ABA1 and ABA-related stress genes. Wild-type germination and gene expression were gradually restored during seed after-ripening, despite of DOF6-induced over-expression. DOF6 was found to interact in a yeast two-hybrid system andin planta with TCP14, a previously described positive regulator of seed germination. The expression of ABA1 and ABA-related stress genes was also enhanced in tcp14 knock-out mutants. Taken together, these results indicate that DOF6 negatively affects seed germination and opposes TCP14 function in the regulation of a specific set of ABA-related genes

Some physical and chemical proceddes in fluids

The ability to reproduce reduced gravity conditions for long periods is one of the reasons why the orbiting laboratory is so attractive. In this paper several fluid dynamics problem areas are reviewed in which zero-gravity conditions are of great importance. Although emphasis is placed on space processing, there are some older problems also in which gravity masks the phenomcna, impeding a reasonably simple approach to the solution. Three problems are considered: Thermal convection under reduced gravity. The dumping effect ofsurface gravity waves at the outset of convection induced by surface tractions is discussed in particular. The existence of convection is of concern for some satellite thermal control techniques presently used, and for most of the proposed manufacturing processes. Whereas convection should be normally avoided, problems related to the containerless stirring ofa melt constitute an exception. Secondly, gravity and chemical reactions. Although chemical reactions are independent of gravity because of the small mass of the molecules and atoms involved, in many cases the reaction rate dcpends on the arrival of the species to the reaction zone. When the arrival process is buoyancy-controlled, the net specd of the reaction will be affected by the gravity. Thirdly, two-phase flows under reduced gravity provkle interesting problems from boiling heat transfer to degasslng of melts. This part of the paper deals only with the measurement of sound veiocity in a liquid containing bubbles. It is suggested that such measurements should be mude under reduced gravity to provide reliable residís.

Metamodelo para la definición, implantación y mejora de los procesos de gestión de proyectos

En los últimos años hemos sido testigos de la creciente demanda de software para resolver problemas cada vez más complejos y de mayor valor agregado. Bajo estas circunstancias, nos podemos hacer la siguiente pregunta: ¿Está preparada la industria de software para entregar el software que se necesita en los próximos años, de acuerdo con las demandas del cliente? Hoy en día, muchos expertos creen que el éxito de esta industria dependerá de su capacidad para gestionar los proyectos, las personas y los recursos. En este sentido, la gestión de proyectos es un factor clave para el éxito de los proyectos software en todo el mundo. Además, considerando que las Pequeñas y Medianas Empresas de software (PYMEs) representan el 99,87% de las empresas españolas, es vital para este tipo de empresas la implementación de los procesos involucrados con la gestión de proyectos. Es cierto que existen muchos modelos que mejoran la eficacia de la gestión de proyectos, pero la mayoría de ellos se centra únicamente en dos procesos: la planificación del proyecto y la monitorización y control del proyecto, ninguno de los cuales a menudo es asequible para las PYMEs. Estos modelos se basan en el consenso de un grupo de trabajo designado para establecer cómo debe ser gestionado el proceso software. Los modelos son bastante útiles ya que proporcionan lineamientos generales sobre dónde empezar a mejorar la gestión de los proyectos, y en qué orden, a personas que no saben cómo hacerlo. Sin embargo, como se ha dicho anteriormente, la mayoría de estos modelos solamente funcionan en escenarios dentro de las grandes empresas. Por lo tanto, es necesario adaptar los modelos y herramientas para el contexto de PYMEs. Esta tesis doctoral presenta una solución complementaria basada en la aplicación de un metamodelo. Este metamodelo es creado para mejorar la calidad de los procesos de la gestión de proyectos a través de la incorporación de prácticas eficaces identificadas a través del análisis y estudio de los modelos y normas existentes relacionadas con la gestión de proyectos. viii ProMEP – Metamodelo para la gestión de proyectos Por lo tanto, el metamodelo PROMEP (Gestión de Proyectos basada en Prácticas Efectivas) permitirá establecer un proceso estándar de gestión de proyectos que puede adaptarse a los proyectos de cada empresa a través de dos pasos: En primer lugar, para obtener una fotografía instantánea (o base) de los procesos de gestión de proyectos de las PYMEs se creó un cuestionario de dos fases para identificar tanto las prácticas realizadas y como las no realizadas. El cuestionario propuesto se basa en el Modelo de Madurez y Capacidad Integrado para el Desarrollo v1.2 (CMMI-DEV v1.2). Como resultado adicional, se espera que la aplicación de este cuestionario ayude a las PYMEs a identificar aquellas prácticas que se llevan a cabo, pero no son documentadas, aquellas que necesitan más atención, y aquellas que no se realizan debido a la mala gestión o al desconocimiento. En segundo lugar, para apoyar fácilmente y eficazmente las tareas de gestión de proyectos software del metamodelo PROMEP, se diseñó una biblioteca de activos de proceso (PAL) para apoyar la definición de los procesos de gestión de proyectos y realizar una gestión cuantitativa de cada proyecto de las PYMEs. Ambos pasos se han implementado como una herramienta computacional que apoya nuestro enfoque de metamodelo. En concreto, la presente investigación propone la construcción del metamodelo PROMEP para aquellas PYMEs que desarrollan productos software de tal forma que les permita planificar, monitorizar y controlar sus proyectos software, identificar los riesgos y tomar las medidas correctivas necesarias, establecer y mantener un conjunto de activos de proceso, definir un mecanismo cuantitativo para predecir el rendimiento de los procesos, y obtener información de mejora. Por lo tanto, nuestro estudio sugiere un metamodelo alternativo para lograr mayores niveles de rendimiento en los entornos de PYMEs. Así, el objetivo principal de esta tesis es ayudar a reducir los excesos de trabajo y el tiempo de entrega, y aumentar así la calidad del software producido en este tipo de organizaciones. Abstract In recent years we have been witnessing the increasing demand for software to solve more and more complex tasks and greater added value. Under these circumstances, we can ourselves the following question: Is the software industry prepared to deliver the software that is needed in the coming years, according to client demands? Nowadays, many experts believe that the industry’ success will depend on its capacity to manage the projects, people and resources. In this sense, project management is a key factor for software project success around the world. Moreover, taking into account that small and medium-sized software enterprises (SMSe) are the 99.87% of the Spanish enterprises, it is vital for this type of enterprises to implement the processes involved in project management. It is true that there are many models that improve the project management effectiveness, but most of them are focused only on two processes: project planning and project monitoring and control, neither of which is affordable for SMSe. Such models are based on the consensus of a designated working group on how software process should be managed. They are very useful in that they provide general guidelines on where to start improving the project management, and in which order, to people who do not know how to do it. However, as we said, the majority of these models have only worked in scenarios within large companies. So, it is necessary to adapt these models and tools to the context of SMSe. A complementary solution based on the implementation of a metamodel is presented in this thesis. This metamodel is created to improve the quality of project management processes through the incorporation of effective practices identified through the analysis and study of relevant models and standards related to project management. Thus, the PROMEP (PROject Management based on Effective Practices) metamodel will allow establishing a project management standard process to be tailored to each enterprise’s project through two steps: Firstly, to obtain a baseline snapshot of project management processes in SMSe a two-phase questionnaire was created to identify both performed and nonperformed practices. The x ProMEP – Metamodelo para la gestión de proyectos proposed questionnaire is based on Capability Maturity Model Integration for Development v1.2. As additional result, it is expected that the application of the questionnaire to the processes will help SMSe to identify those practices which are performed but not documented, which practices need more attention, and which are not implemented due to bad management or unawareness. Secondly, to easily an effectively support the software project management tasks in the PROMEP metamodel, a Process Asset Library (PAL) is designed to support the definition of project management processes and to achieve quantitative project management in SMSe. Both steps have been implemented as a computational tool that supports our metamodel approach. Concretely, the present research proposes the accomplishment of the PROMEP metamodel for those SMSe which develop software products and enable them to plan, supervise and control their software projects, identify risks and take corrective actions, establish and maintain a set of process assets, define quantitative models that predict the process performance, and provide improvement information. So, our study suggests an alternative metamodel to achieve higher performance levels in the SMSe environments. The main objective of this thesis is help to reduce software overruns and delivery time, and increase software quality in these types of organizations.

Análisis genómico y funcional de los sistemas de Quorum Sensing en Rhizobium leguminosarum

Rhizobium leguminosarum (Rl) es una alfa-proteobacteria capaz de establecer una simbiosis diazotrófica con distintas leguminosas. A pesar de la importancia de esta simbiosis en el balance global del ciclo del nitrógeno, muy pocos genomas de rhizobios han sido secuenciados, que aporten nuevos conocimientos relacionados con las características genéticas que contribuyen a importantes procesos simbióticos. Únicamente tres secuencias completas de Rl han sido publicadas: Rl bv. viciae 3841 y dos genomas de Rl bv. trifolii (WSM1325 y WSM2304), ambos simbiontes de trébol. La secuencia genómica de Rlv UPM791 se ha determinado por medio de secuenciación 454. Este genoma tiene un tamaño aproximado de 7.8 Mb, organizado en un cromosoma y 5 replicones extracromosómicos, que incluyen un plásmido simbiótico de 405 kb. Este nuevo genoma se ha analizado en relación a las funciones simbióticas y adaptativas en comparación con los genomas completos de Rlv 3841 y Rl bv. trifolii WSM1325 y WSM2304. Mientras que los plásmidos pUPM791a y b se encuentran conservados, el plásmido simbiótico pUPM791c exhibe un grado de conservación muy bajo comparado con aquellos descritos en las otras cepas de Rl. Uno de los factores implicados en el establecimiento de la simbiosis es el sistema de comunicación intercelular conocido como Quorum Sensing (QS). El análisis del genoma de Rlv UPM791 ha permitido la identificación de dos sistemas tipo LuxRI mediados por señales de tipo N-acyl-homoserina lactonas (AHLs). El análisis mediante HPLC-MS ha permitido asociar las señales C6-HSL, C7-HSL y C8-HSL al sistema rhiRI, codificado en el plásmido simbiótico; mientras que el sistema cinRI, localizado en el cromosoma, produce 3OH-C14:1-HSL. Se ha identificado una tercera sintasa (TraI) codificada en el plásmido simbiótico, pero su regulador correspondiente se encuentra truncado debido a un salto de fase. Adicionalmente, se han encontrado tres reguladores de tipo LuxR-orphan que no presentan una sintasa LuxI asociada. El efecto potencial de las señales tipo AHL se ha estudiado mediante una estrategia de quorum quenching, la cual interfiere con los sistemas de QS de la bacteria. Esta estrategia está basada en la introducción del gen aiiA de Bacillus subtilis, que expresa constitutivamente una enzima lactonasa degradadora de AHLs. Para llevar a cabo el análisis en condiciones simbióticas, se ha desarrollado un sistema de doble marcaje que permite la identificación basado en los marcadores gusA y celB, que codifican para una enzima β–glucuronidasa y una β–galactosidasa termoestable, respectivamente. Los resultados obtenidos indican que Rlv UPM791 predomina sobre la cepa Rlv 3841 para la formación de nódulos en plantas de guisante. La baja estabilidad del plásmido que codifica para aiiA, no ha permitido obtener una conclusión definitiva sobre el efecto de la lactonasa AiiA en competitividad. Con el fin de analizar el significado y la regulación de la producción de moléculas señal tipo AHL, se han generado mutantes defectivos en cada uno de los dos sistemas de QS. Se ha llevado a cabo un análisis detallado sobre la producción de AHLs, formación de biofilm y simbiosis con plantas de guisante, veza y lenteja. El efecto de las deleciones de los genes rhiI y rhiR en Rlv UPM791 es más drástico en ausencia del plásmido pUPM791d. Mutaciones en cinI o cinRIS muestran tanto ausencia de señales, como producción exclusivamente de las de bajo peso molecular, respectivamente, producidas por el sistema rhiRI. Estas mutaciones mostraron un efecto importante en simbiosis. El sistema rhiRI se necesita para un comportamiento simbiótico normal. Además, mutantes cinRIS generaron nódulos blancos e ineficientes, mientras que el mutante cinI fue incapaz de producir nódulos en ninguna de las leguminosas utilizadas. Dicha mutación resultó en la inestabilización del plasmido simbiótico por un mecanismo dependiente de cinI que no ha sido aclarado. En general, los resultados obtenidos indican la existencia de un modelo de regulación dependiente de QS significativamente distinto a los que se han descrito previamente en otras cepas de R. leguminosarum, en las cuales no se había observado ningún fenotipo relevante en simbiosis. La regulación de la producción de AHLs Rlv UPM791 es un proceso complejo que implica genes situados en los plásmidos UPM791c y UPM791d, además de la señal 3-OH-C14:1-HSL. Finalmente, se ha identificado un transportador de tipo RND, homologo a mexAB-oprM de P. aeruginosa e implicado en la extrusión de AHLs de cadena larga. La mutación he dicho transportador no tuvo efectos apreciables sobre la simbiosis. ABSTRACT Rhizobium leguminosarum (Rl) is a soil alpha-proteobacterium that establishes a diazotrophic symbiosis with different legumes. Despite the importance of this symbiosis to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far which provide new insights into the genetic features contributing to symbiotically relevant processes. Only three complete sequences of Rl strains have been published: Rl bv. viciae 3841, harboring six plasmids (7.75 Mb) and two Rl bv. trifolii (WSM1325 and WSM2304), both clover symbionts, harboring 5 and 4 plasmids, respectively (7.41 and 6.87 Mb). The genomic sequence of Rlv UPM791 was undertaken by means of 454 sequencing. Illumina and Sanger reads were used to improve the assembly, leading to 17 final contigs. This genome has an estimated size of 7.8 Mb organized in one chromosome and five extrachromosomal replicons, including a 405 kb symbiotic plasmid. Four of these plasmids are already closed, whereas there are still gaps in the smallest one (pUPM791d) due to the presence of insertion elements and repeated sequences, which difficult the assembly. The annotation has been carried out thanks to the Manatee pipeline. This new genome has been analyzed as regarding symbiotic and adaptive functions in comparison to the Rlv 3841 complete genome, and to those from Rl bv. trifolii strains WSM1325 and WSM2304. While plasmids pUPM791a and b are conserved, the symbiotic plasmid pUPM791c exhibited the lowest degree of conservation as compared to those from the other Rl strains. One of the factors involved in the symbiotic process is the intercellular communication system known as Quorum Sensing (QS). This mechanism allows bacteria to carry out diverse biological processes in a coordinate way through the production and detection of extracellular signals that regulate the transcription of different target genes. Analysis of the Rlv UPM791 genome allowed the identification of two LuxRI-like systems mediated by N-acyl-homoserine lactones (AHLs). HPLC-MS analysis allowed the adscription of C6-HSL, C7-HSL and C8-HSL signals to the rhiRI system, encoded in the symbiotic plasmid, whereas the cinRI system, located in the chromosome, produces 3OH-C14:1-HSL, previously described as “bacteriocin small”. A third synthase (TraI) is encoded also in the symbiotic plasmid, but its cognate regulator TraR is not functional due to a fameshift mutation. Three additional LuxR orphans were also found which no associated LuxI-type synthase. The potential effect of AHLs has been studied by means of a quorum quenching approach to interfere with the QS systems of the bacteria. This approach is based upon the introduction into the strains Rl UPM791 and Rl 3841 of the Bacillus subtilis gene aiiA expressing constitutively an AHL-degrading lactonase enzyme which led to virtual absence of AHL even when AiiA-expressing cells were a fraction of the total population. No significant effect of AiiA-mediated AHL removal on competitiveness for growth in solid surface was observed. For analysis under symbiotic conditions we have set up a two-label system to identify nodules produced by two different strains in pea roots, based on the markers gusA and celB, encoding a β–glucuronidase and a thermostable β–galactosidase enzymes, respectively. The results obtained show that Rlv UPM791 outcompetes Rlv 3841 for nodule formation in pea plants, and that the presence of the AiiA plasmid does not significantly affect the relative competitiveness of the two Rlv strains. However, the low stability of the pME6863 plasmid, encoding aiiA, did not lead to a clear conclusion about the AiiA lactonase effect on competitiveness. In order to further analyze the significance and regulation of the production of AHL signal molecules, mutants deficient in each of the two QS systems were constructed. A detailed analysis of the effect of these mutations on AHL production, biofilm formation and symbiosis with pea, vetch and lentil plants has been carried out. The effect of deletions on Rlv UPM791 rhiI and rhiR genes is more pronounced in the absence of plasmid pUPM791d, as no signal is detected in UPM791.1, lacking this plasmid. Mutations in cinI or cinRIS show either no signals, or only the small ones produced by the rhiRI system, suggesting that cinR might be regulating the rhiRI system. These mutations had a strong effect on symbiosis. Analysis of rhi mutants revealed that rhiRI system is required for normal symbiotic performance, as a drastic reduction of symbiotic fitness is observed when rhiI is deleted, and rhiR is essential for nitrogen fixation in the absence of plasmid pUPM791d. Furthermore, cinRIS mutants resulted in white and inefficient nodules, whereas cinI mutant was unable to form nodules on any legume tested. The latter mutation is associated to the instabilization of the symbiotic plasmid through a mechanism still uncovered. Overall, the results obtained indicate the existence of a model of QS-dependent regulation significantly different to that previously described in other R. leguminosarum strains, where no relevant symbiotic phenotype had been observed. The regulation of AHL production in Rlv UPM791 is a complex process involving the symbiotic plasmid (pUPM791c) and the smallest plasmid (pUPM791d), with a key role for the 3-OH-C14:1-HSL signal. Finally, we made a search for potential AHL transporters in Rlv UPM791 genome. These signals diffuse freely across membranes, but in the case of the long-chain AHLs an active efflux system might be required, as it has been described for C12-HSL in the case of Pseudomonas aeruginosa. We have identified a putative AHL transporter of the RND family homologous to P. aeruginosa mexAB-oprM. A mutant strain deficient in this transporter has been generated, and TLC analysis shows absence of 3OH-C14:1-HSL in its supernatant. This deficiency was complemented by the reintroduction of an intact copy of the genes via plasmid transfer. The mutation in mexAB genes had no significant effects on the symbiotic performance of R. leguminosarum bv. viciae.

Functional and effective connectivity in MEG. Application to the study of epilepsy

Nuestro cerebro contiene cerca de 1014 sinapsis neuronales. Esta enorme cantidad de conexiones proporciona un entorno ideal donde distintos grupos de neuronas se sincronizan transitoriamente para provocar la aparición de funciones cognitivas, como la percepción, el aprendizaje o el pensamiento. Comprender la organización de esta compleja red cerebral en base a datos neurofisiológicos, representa uno de los desafíos más importantes y emocionantes en el campo de la neurociencia. Se han propuesto recientemente varias medidas para evaluar cómo se comunican las diferentes partes del cerebro a diversas escalas (células individuales, columnas corticales, o áreas cerebrales). Podemos clasificarlos, según su simetría, en dos grupos: por una parte, la medidas simétricas, como la correlación, la coherencia o la sincronización de fase, que evalúan la conectividad funcional (FC); mientras que las medidas asimétricas, como la causalidad de Granger o transferencia de entropía, son capaces de detectar la dirección de la interacción, lo que denominamos conectividad efectiva (EC). En la neurociencia moderna ha aumentado el interés por el estudio de las redes funcionales cerebrales, en gran medida debido a la aparición de estos nuevos algoritmos que permiten analizar la interdependencia entre señales temporales, además de la emergente teoría de redes complejas y la introducción de técnicas novedosas, como la magnetoencefalografía (MEG), para registrar datos neurofisiológicos con gran resolución. Sin embargo, nos hallamos ante un campo novedoso que presenta aun varias cuestiones metodológicas sin resolver, algunas de las cuales trataran de abordarse en esta tesis. En primer lugar, el creciente número de aproximaciones para determinar la existencia de FC/EC entre dos o más señales temporales, junto con la complejidad matemática de las herramientas de análisis, hacen deseable organizarlas todas en un paquete software intuitivo y fácil de usar. Aquí presento HERMES (http://hermes.ctb.upm.es), una toolbox en MatlabR, diseñada precisamente con este fin. Creo que esta herramienta será de gran ayuda para todos aquellos investigadores que trabajen en el campo emergente del análisis de conectividad cerebral y supondrá un gran valor para la comunidad científica. La segunda cuestión practica que se aborda es el estudio de la sensibilidad a las fuentes cerebrales profundas a través de dos tipos de sensores MEG: gradiómetros planares y magnetómetros, esta aproximación además se combina con un enfoque metodológico, utilizando dos índices de sincronización de fase: phase locking value (PLV) y phase lag index (PLI), este ultimo menos sensible a efecto la conducción volumen. Por lo tanto, se compara su comportamiento al estudiar las redes cerebrales, obteniendo que magnetómetros y PLV presentan, respectivamente, redes más densamente conectadas que gradiómetros planares y PLI, por los valores artificiales que crea el problema de la conducción de volumen. Sin embargo, cuando se trata de caracterizar redes epilépticas, el PLV ofrece mejores resultados, debido a la gran dispersión de las redes obtenidas con PLI. El análisis de redes complejas ha proporcionado nuevos conceptos que mejoran caracterización de la interacción de sistemas dinámicos. Se considera que una red está compuesta por nodos, que simbolizan sistemas, cuyas interacciones se representan por enlaces, y su comportamiento y topología puede caracterizarse por un elevado número de medidas. Existe evidencia teórica y empírica de que muchas de ellas están fuertemente correlacionadas entre sí. Por lo tanto, se ha conseguido seleccionar un pequeño grupo que caracteriza eficazmente estas redes, y condensa la información redundante. Para el análisis de redes funcionales, la selección de un umbral adecuado para decidir si un determinado valor de conectividad de la matriz de FC es significativo y debe ser incluido para un análisis posterior, se convierte en un paso crucial. En esta tesis, se han obtenido resultados más precisos al utilizar un test de subrogadas, basado en los datos, para evaluar individualmente cada uno de los enlaces, que al establecer a priori un umbral fijo para la densidad de conexiones. Finalmente, todas estas cuestiones se han aplicado al estudio de la epilepsia, caso práctico en el que se analizan las redes funcionales MEG, en estado de reposo, de dos grupos de pacientes epilépticos (generalizada idiopática y focal frontal) en comparación con sujetos control sanos. La epilepsia es uno de los trastornos neurológicos más comunes, con más de 55 millones de afectados en el mundo. Esta enfermedad se caracteriza por la predisposición a generar ataques epilépticos de actividad neuronal anormal y excesiva o bien síncrona, y por tanto, es el escenario perfecto para este tipo de análisis al tiempo que presenta un gran interés tanto desde el punto de vista clínico como de investigación. Los resultados manifiestan alteraciones especificas en la conectividad y un cambio en la topología de las redes en cerebros epilépticos, desplazando la importancia del ‘foco’ a la ‘red’, enfoque que va adquiriendo relevancia en las investigaciones recientes sobre epilepsia. ABSTRACT There are about 1014 neuronal synapses in the human brain. This huge number of connections provides the substrate for neuronal ensembles to become transiently synchronized, producing the emergence of cognitive functions such as perception, learning or thinking. Understanding the complex brain network organization on the basis of neuroimaging data represents one of the most important and exciting challenges for systems neuroscience. Several measures have been recently proposed to evaluate at various scales (single cells, cortical columns, or brain areas) how the different parts of the brain communicate. We can classify them, according to their symmetry, into two groups: symmetric measures, such as correlation, coherence or phase synchronization indexes, evaluate functional connectivity (FC); and on the other hand, the asymmetric ones, such as Granger causality or transfer entropy, are able to detect effective connectivity (EC) revealing the direction of the interaction. In modern neurosciences, the interest in functional brain networks has increased strongly with the onset of new algorithms to study interdependence between time series, the advent of modern complex network theory and the introduction of powerful techniques to record neurophysiological data, such as magnetoencephalography (MEG). However, when analyzing neurophysiological data with this approach several questions arise. In this thesis, I intend to tackle some of the practical open problems in the field. First of all, the increase in the number of time series analysis algorithms to study brain FC/EC, along with their mathematical complexity, creates the necessity of arranging them into a single, unified toolbox that allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of them. I developed such a toolbox for this aim, it is named HERMES (http://hermes.ctb.upm.es), and encompasses several of the most common indexes for the assessment of FC and EC running for MatlabR environment. I believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis and will entail a great value for the scientific community. The second important practical issue tackled in this thesis is the evaluation of the sensitivity to deep brain sources of two different MEG sensors: planar gradiometers and magnetometers, in combination with the related methodological approach, using two phase synchronization indexes: phase locking value (PLV) y phase lag index (PLI), the latter one being less sensitive to volume conduction effect. Thus, I compared their performance when studying brain networks, obtaining that magnetometer sensors and PLV presented higher artificial values as compared with planar gradiometers and PLI respectively. However, when it came to characterize epileptic networks it was the PLV which gives better results, as PLI FC networks where very sparse. Complex network analysis has provided new concepts which improved characterization of interacting dynamical systems. With this background, networks could be considered composed of nodes, symbolizing systems, whose interactions with each other are represented by edges. A growing number of network measures is been applied in network analysis. However, there is theoretical and empirical evidence that many of these indexes are strongly correlated with each other. Therefore, in this thesis I reduced them to a small set, which could more efficiently characterize networks. Within this framework, selecting an appropriate threshold to decide whether a certain connectivity value of the FC matrix is significant and should be included in the network analysis becomes a crucial step, in this thesis, I used the surrogate data tests to make an individual data-driven evaluation of each of the edges significance and confirmed more accurate results than when just setting to a fixed value the density of connections. All these methodologies were applied to the study of epilepsy, analysing resting state MEG functional networks, in two groups of epileptic patients (generalized and focal epilepsy) that were compared to matching control subjects. Epilepsy is one of the most common neurological disorders, with more than 55 million people affected worldwide, characterized by its predisposition to generate epileptic seizures of abnormal excessive or synchronous neuronal activity, and thus, this scenario and analysis, present a great interest from both the clinical and the research perspective. Results revealed specific disruptions in connectivity and network topology and evidenced that networks’ topology is changed in epileptic brains, supporting the shift from ‘focus’ to ‘networks’ which is gaining importance in modern epilepsy research.

Maintaining distances with the engineer: patterns of coexistence in plant communities beyond the patch-bare dichotomy

Two-phase plant communities with an engineer conforming conspicuous patches and affecting the performance and patterns of coexisting species are the norm under stressful conditions. To unveil the mechanisms governing coexistence in these communities at multiple spatial scales, we have developed a new point-raster approach of spatial pattern analysis, which was applied to a Mediterranean high mountain grassland to show how Festuca curvifolia patches affect the local distribution of coexisting species. We recorded 22 111 individuals of 17 plant perennial species. Most coexisting species were negatively associated with F. curvifolia clumps. Nevertheless, bivariate nearest-neighbor analyses revealed that the majority of coexisting species were confined at relatively short distances from F. curvifolia borders (between 0-2 cm and up to 8 cm in some cases). Our study suggests the existence of a fine-scale effect of F. curvifolia for most species promoting coexistence through a mechanism we call 'facilitation in the halo'. Most coexisting species are displaced to an interphase area between patches, where two opposite forces reach equilibrium: attenuated severe conditions by proximity to the F. curvifolia canopy (nutrient-rich islands) and competitive exclusion mitigated by avoiding direct contact with F. curvifolia.

Negative density dependence and environmental heterogeneity effects on tree ferns across succession in a tropical montane forest.

Although tree ferns are an important component of temperate and tropical forests, very little is known about their ecology. Their peculiar biology (e.g., dispersal by spores and two-phase life cycle) makes it difficult to extrapolate current knowledge on the ecology of other tree species to tree ferns. In this paper, we studied the effects of negative density dependence (NDD) and environmental heterogeneity on populations of two abundant tree fern species, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient. Species patterns harbor information on processes such as competition that can be easily revealed using point pattern analysis techniques. However, its detection may be difficult due to the confounded effects of habitat heterogeneity. Here, we mapped three forest plots along a successional gradient in the montane forests of Southern Ecuador. We employed homogeneous and inhomogeneous K and pair correlation functions to quantify the change in the spatial pattern of different size classes and a case-control design to study associations between juvenile and adult tree ferns. Using spatial estimates of the biomass of four functional tree types (short- and long-lived pioneer, shade- and partial shade-tolerant) as covariates, we fitted heterogeneous Poisson models to the point pattern of juvenile and adult tree ferns and explored the existence of habitat dependencies on these patterns. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities.

Diseño de separadores mediante aplicación informática = Computer Application for Sepators Design

Programa informático desarrollado en plataforma EXCEL (VBA) y dirigido al diseño de Separadores de dos y tres fases, verticales y horizontales. El programa de ordenador o aplicación tiene la capacidad de determinar las propiedades físicas del fluido, utilizando diferentes correlaciones sobre la base del “Black Oil Model”, con dichas propiedades el Programa predice el tipo de flujo presente. Si el tipo de flujo es “Slug Flow” el programa determinara las dimensiones del “Slug catcher” necesario. Bajo las condiciones de funcionamiento existentes el programa diseñará el separador elegido: dos o tres fases, vertical u horizontal. Por último, la aplicación informática estimará el coste del equipo. Abstract Computer program developed in EXCEL (VBA) platform and aimed for the design of Two-Phase, Three-Phase, Vertical or Horizontal Separators. The computer Program or Application has the capability to determine the fluid physical properties utilizing different correlations on the basis of the Black Oil Model, with those Properties the Program will predict the Flow Regime present. If the flow regime is Slug Flow the program will determine the necessary slug catcher dimensions. Under certain operational conditions the program will design the selected: Two-Phase or Three-Phase, Vertical or Horizontal Separator. Finally the computer Application will estimate the cost of the equipment.

Agrobacterium VirD2 protein interacts with plant host cyclophilins

Agrobacterium tumefaciens induces crown gall tumors on plants by transferring a nucleoprotein complex, the T-complex, from the bacterium to the plant cell. The T-complex consists of T-DNA, a single-stranded DNA segment of the tumor-inducing plasmid, VirD2, an endonuclease covalently bound to the 5′ end of the T-DNA, and perhaps VirE2, a single-stranded DNA binding protein. The yeast two-hybrid system was used to screen for proteins interacting with VirD2 and VirE2 to identify components in Arabidopsis thaliana that interact with the T-complex. Three VirD2- and two VirE2-interacting proteins were identified. Here we characterize the interactions of VirD2 with two isoforms of Arabidopsis cyclophilins identified by using this analysis. The VirD2 domain interacting with the cyclophilins is distinct from the endonuclease, omega, and the nuclear localization signal domains. The VirD2–cyclophilin interaction is disrupted in vitro by cyclosporin A, which also inhibits Agrobacterium-mediated transformation of Arabidopsis and tobacco. These data strongly suggest that host cyclophilins play a role in T-DNA transfer.