Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.

GreenDisc: a HW/SW energy optimization framework in globally distributed computation

In recent future, wireless sensor networks (WSNs) will experience a broad high-scale deployment (millions of nodes in the national area) with multiple information sources per node, and with very specific requirements for signal processing. In parallel, the broad range deployment of WSNs facilitates the definition and execution of ambitious studies, with a large input data set and high computational complexity. These computation resources, very often heterogeneous and driven on-demand, can only be satisfied by high-performance Data Centers (DCs). The high economical and environmental impact of the energy consumption in DCs requires aggressive energy optimization policies. These policies have been already detected but not successfully proposed. In this context, this paper shows the following on-going research lines and obtained results. In the field of WSNs: energy optimization in the processing nodes from different abstraction levels, including reconfigurable application specific architectures, efficient customization of the memory hierarchy, energy-aware management of the wireless interface, and design automation for signal processing applications. In the field of DCs: energy-optimal workload assignment policies in heterogeneous DCs, resource management policies with energy consciousness, and efficient cooling mechanisms that will cooperate in the minimization of the electricity bill of the DCs that process the data provided by the WSNs.

GreenDisc: a HW/SW energy optimization framework in globally distributed computation

In recent future, wireless sensor networks ({WSNs}) will experience a broad high-scale deployment (millions of nodes in the national area) with multiple information sources per node, and with very specific requirements for signal processing. In parallel, the broad range deployment of {WSNs} facilitates the definition and execution of ambitious studies, with a large input data set and high computational complexity. These computation resources, very often heterogeneous and driven on-demand, can only be satisfied by high-performance Data Centers ({DCs}). The high economical and environmental impact of the energy consumption in {DCs} requires aggressive energy optimization policies. These policies have been already detected but not successfully proposed. In this context, this paper shows the following on-going research lines and obtained results. In the field of {WSNs}: energy optimization in the processing nodes from different abstraction levels, including reconfigurable application specific architectures, efficient customization of the memory hierarchy, energy-aware management of the wireless interface, and design automation for signal processing applications. In the field of {DCs}: energy-optimal workload assignment policies in heterogeneous {DCs}, resource management policies with energy consciousness, and efficient cooling mechanisms that will cooperate in the minimization of the electricity bill of the DCs that process the data provided by the WSNs.

Methodologies for Collision Risk Computation = Metodologías para Cálculo de Riesgo de Colisión

Esta tesis aborda metodologías para el cálculo de riesgo de colisión de satélites. La minimización del riesgo de colisión se debe abordar desde dos puntos de vista distintos. Desde el punto de vista operacional, es necesario filtrar los objetos que pueden presentar un encuentro entre todos los objetos que comparten el espacio con un satélite operacional. Puesto que las órbitas, del objeto operacional y del objeto envuelto en la colisión, no se conocen perfectamente, la geometría del encuentro y el riesgo de colisión deben ser evaluados. De acuerdo con dicha geometría o riesgo, una maniobra evasiva puede ser necesaria para evitar la colisión. Dichas maniobras implican un consumo de combustible que impacta en la capacidad de mantenimiento orbital y por tanto de la visa útil del satélite. Por tanto, el combustible necesario a lo largo de la vida útil de un satélite debe ser estimado en fase de diseño de la misión para una correcta definición de su vida útil, especialmente para satélites orbitando en regímenes orbitales muy poblados. Los dos aspectos, diseño de misión y aspectos operacionales en relación con el riesgo de colisión están abordados en esta tesis y se resumen en la Figura 3. En relación con los aspectos relacionados con el diseño de misión (parte inferior de la figura), es necesario evaluar estadísticamente las características de de la población espacial y las teorías que permiten calcular el número medio de eventos encontrados por una misión y su capacidad de reducir riesgo de colisión. Estos dos aspectos definen los procedimientos más apropiados para reducir el riesgo de colisión en fase operacional. Este aspecto es abordado, comenzando por la teoría descrita en [Sánchez-Ortiz, 2006]T.14 e implementada por el autor de esta tesis en la herramienta ARES [Sánchez-Ortiz, 2004b]T.15 proporcionada por ESA para la evaluación de estrategias de evitación de colisión. Esta teoría es extendida en esta tesis para considerar las características de los datos orbitales disponibles en las fases operacionales de un satélite (sección 4.3.3). Además, esta teoría se ha extendido para considerar riesgo máximo de colisión cuando la incertidumbre de las órbitas de objetos catalogados no es conocida (como se da el caso para los TLE), y en el caso de querer sólo considerar riesgo de colisión catastrófico (sección 4.3.2.3). Dichas mejoras se han incluido en la nueva versión de ARES [Domínguez-González and Sánchez-Ortiz, 2012b]T.12 puesta a disposición a través de [SDUP,2014]R.60. En fase operacional, los catálogos que proporcionan datos orbitales de los objetos espaciales, son procesados rutinariamente, para identificar posibles encuentros que se analizan en base a algoritmos de cálculo de riesgo de colisión para proponer maniobras de evasión. Actualmente existe una única fuente de datos públicos, el catálogo TLE (de sus siglas en inglés, Two Line Elements). Además, el Joint Space Operation Center (JSpOC) Americano proporciona mensajes con alertas de colisión (CSM) cuando el sistema de vigilancia americano identifica un posible encuentro. En función de los datos usados en fase operacional (TLE o CSM), la estrategia de evitación puede ser diferente debido a las características de dicha información. Es preciso conocer las principales características de los datos disponibles (respecto a la precisión de los datos orbitales) para estimar los posibles eventos de colisión encontrados por un satélite a lo largo de su vida útil. En caso de los TLE, cuya precisión orbital no es proporcionada, la información de precisión orbital derivada de un análisis estadístico se puede usar también en el proceso operacional así como en el diseño de la misión. En caso de utilizar CSM como base de las operaciones de evitación de colisiones, se conoce la precisión orbital de los dos objetos involucrados. Estas características se han analizado en detalle, evaluando estadísticamente las características de ambos tipos de datos. Una vez concluido dicho análisis, se ha analizado el impacto de utilizar TLE o CSM en las operaciones del satélite (sección 5.1). Este análisis se ha publicado en una revista especializada [Sánchez-Ortiz, 2015b]T.3. En dicho análisis, se proporcionan recomendaciones para distintas misiones (tamaño del satélite y régimen orbital) en relación con las estrategias de evitación de colisión para reducir el riesgo de colisión de manera significativa. Por ejemplo, en el caso de un satélite en órbita heliosíncrona en régimen orbital LEO, el valor típico del ACPL que se usa de manera extendida es 10-4. Este valor no es adecuado cuando los esquemas de evitación de colisión se realizan sobre datos TLE. En este caso, la capacidad de reducción de riesgo es prácticamente nula (debido a las grandes incertidumbres de los datos TLE) incluso para tiempos cortos de predicción. Para conseguir una reducción significativa del riesgo, sería necesario usar un ACPL en torno a 10-6 o inferior, produciendo unas 10 alarmas al año por satélite (considerando predicciones a un día) o 100 alarmas al año (con predicciones a tres días). Por tanto, la principal conclusión es la falta de idoneidad de los datos TLE para el cálculo de eventos de colisión. Al contrario, usando los datos CSM, debido a su mejor precisión orbital, se puede obtener una reducción significativa del riesgo con ACPL en torno a 10-4 (considerando 3 días de predicción). Incluso 5 días de predicción pueden ser considerados con ACPL en torno a 10-5. Incluso tiempos de predicción más largos se pueden usar (7 días) con reducción del 90% del riesgo y unas 5 alarmas al año (en caso de predicciones de 5 días, el número de maniobras se mantiene en unas 2 al año). La dinámica en GEO es diferente al caso LEO y hace que el crecimiento de las incertidumbres orbitales con el tiempo de propagación sea menor. Por el contrario, las incertidumbres derivadas de la determinación orbital son peores que en LEO por las diferencias en las capacidades de observación de uno y otro régimen orbital. Además, se debe considerar que los tiempos de predicción considerados para LEO pueden no ser apropiados para el caso de un satélite GEO (puesto que tiene un periodo orbital mayor). En este caso usando datos TLE, una reducción significativa del riesgo sólo se consigue con valores pequeños de ACPL, produciendo una alarma por año cuando los eventos de colisión se predicen a un día vista (tiempo muy corto para implementar maniobras de evitación de colisión).Valores más adecuados de ACPL se encuentran entre 5•10-8 y 10-7, muy por debajo de los valores usados en las operaciones actuales de la mayoría de las misiones GEO (de nuevo, no se recomienda en este régimen orbital basar las estrategias de evitación de colisión en TLE). Los datos CSM permiten una reducción de riesgo apropiada con ACPL entre 10-5 y 10-4 con tiempos de predicción cortos y medios (10-5 se recomienda para predicciones a 5 o 7 días). El número de maniobras realizadas sería una en 10 años de misión. Se debe notar que estos cálculos están realizados para un satélite de unos 2 metros de radio. En el futuro, otros sistemas de vigilancia espacial (como el programa SSA de la ESA), proporcionarán catálogos adicionales de objetos espaciales con el objetivo de reducir el riesgo de colisión de los satélites. Para definir dichos sistemas de vigilancia, es necesario identificar las prestaciones del catalogo en función de la reducción de riesgo que se pretende conseguir. Las características del catálogo que afectan principalmente a dicha capacidad son la cobertura (número de objetos incluidos en el catalogo, limitado principalmente por el tamaño mínimo de los objetos en función de las limitaciones de los sensores utilizados) y la precisión de los datos orbitales (derivada de las prestaciones de los sensores en relación con la precisión de las medidas y la capacidad de re-observación de los objetos). El resultado de dicho análisis (sección 5.2) se ha publicado en una revista especializada [Sánchez-Ortiz, 2015a]T.2. Este análisis no estaba inicialmente previsto durante la tesis, y permite mostrar como la teoría descrita en esta tesis, inicialmente definida para facilitar el diseño de misiones (parte superior de la figura 1) se ha extendido y se puede aplicar para otros propósitos como el dimensionado de un sistema de vigilancia espacial (parte inferior de la figura 1). La principal diferencia de los dos análisis se basa en considerar las capacidades de catalogación (precisión y tamaño de objetos observados) como una variable a modificar en el caso de un diseño de un sistema de vigilancia), siendo fijas en el caso de un diseño de misión. En el caso de las salidas generadas en el análisis, todos los aspectos calculados en un análisis estadístico de riesgo de colisión son importantes para diseño de misión (con el objetivo de calcular la estrategia de evitación y la cantidad de combustible a utilizar), mientras que en el caso de un diseño de un sistema de vigilancia, los aspectos más importantes son el número de maniobras y falsas alarmas (fiabilidad del sistema) y la capacidad de reducción de riesgo (efectividad del sistema). Adicionalmente, un sistema de vigilancia espacial debe ser caracterizado por su capacidad de evitar colisiones catastróficas (evitando así in incremento dramático de la población de basura espacial), mientras que el diseño de una misión debe considerar todo tipo de encuentros, puesto que un operador está interesado en evitar tanto las colisiones catastróficas como las letales. Del análisis de las prestaciones (tamaño de objetos a catalogar y precisión orbital) requeridas a un sistema de vigilancia espacial se concluye que ambos aspectos han de ser fijados de manera diferente para los distintos regímenes orbitales. En el caso de LEO se hace necesario observar objetos de hasta 5cm de radio, mientras que en GEO se rebaja este requisito hasta los 100 cm para cubrir las colisiones catastróficas. La razón principal para esta diferencia viene de las diferentes velocidades relativas entre los objetos en ambos regímenes orbitales. En relación con la precisión orbital, ésta ha de ser muy buena en LEO para poder reducir el número de falsas alarmas, mientras que en regímenes orbitales más altos se pueden considerar precisiones medias. En relación con los aspectos operaciones de la determinación de riesgo de colisión, existen varios algoritmos de cálculo de riesgo entre dos objetos espaciales. La Figura 2 proporciona un resumen de los casos en cuanto a algoritmos de cálculo de riesgo de colisión y como se abordan en esta tesis. Normalmente se consideran objetos esféricos para simplificar el cálculo de riesgo (caso A). Este caso está ampliamente abordado en la literatura y no se analiza en detalle en esta tesis. Un caso de ejemplo se proporciona en la sección 4.2. Considerar la forma real de los objetos (caso B) permite calcular el riesgo de una manera más precisa. Un nuevo algoritmo es definido en esta tesis para calcular el riesgo de colisión cuando al menos uno de los objetos se considera complejo (sección 4.4.2). Dicho algoritmo permite calcular el riesgo de colisión para objetos formados por un conjunto de cajas, y se ha presentado en varias conferencias internacionales. Para evaluar las prestaciones de dicho algoritmo, sus resultados se han comparado con un análisis de Monte Carlo que se ha definido para considerar colisiones entre cajas de manera adecuada (sección 4.1.2.3), pues la búsqueda de colisiones simples aplicables para objetos esféricos no es aplicable a este caso. Este análisis de Monte Carlo se considera la verdad a la hora de calcular los resultados del algoritmos, dicha comparativa se presenta en la sección 4.4.4. En el caso de satélites que no se pueden considerar esféricos, el uso de un modelo de la geometría del satélite permite descartar eventos que no son colisiones reales o estimar con mayor precisión el riesgo asociado a un evento. El uso de estos algoritmos con geometrías complejas es más relevante para objetos de dimensiones grandes debido a las prestaciones de precisión orbital actuales. En el futuro, si los sistemas de vigilancia mejoran y las órbitas son conocidas con mayor precisión, la importancia de considerar la geometría real de los satélites será cada vez más relevante. La sección 5.4 presenta un ejemplo para un sistema de grandes dimensiones (satélite con un tether). Adicionalmente, si los dos objetos involucrados en la colisión tienen velocidad relativa baja (y geometría simple, Caso C en la Figura 2), la mayor parte de los algoritmos no son aplicables requiriendo implementaciones dedicadas para este caso particular. En esta tesis, uno de estos algoritmos presentado en la literatura [Patera, 2001]R.26 se ha analizado para determinar su idoneidad en distintos tipos de eventos (sección 4.5). La evaluación frete a un análisis de Monte Carlo se proporciona en la sección 4.5.2. Tras este análisis, se ha considerado adecuado para abordar las colisiones de baja velocidad. En particular, se ha concluido que el uso de algoritmos dedicados para baja velocidad son necesarios en función del tamaño del volumen de colisión proyectado en el plano de encuentro (B-plane) y del tamaño de la incertidumbre asociada al vector posición entre los dos objetos. Para incertidumbres grandes, estos algoritmos se hacen más necesarios pues la duración del intervalo en que los elipsoides de error de los dos objetos pueden intersecar es mayor. Dicho algoritmo se ha probado integrando el algoritmo de colisión para objetos con geometrías complejas. El resultado de dicho análisis muestra que este algoritmo puede ser extendido fácilmente para considerar diferentes tipos de algoritmos de cálculo de riesgo de colisión (sección 4.5.3). Ambos algoritmos, junto con el método Monte Carlo para geometrías complejas, se han implementado en la herramienta operacional de la ESA CORAM, que es utilizada para evaluar el riesgo de colisión en las actividades rutinarias de los satélites operados por ESA [Sánchez-Ortiz, 2013a]T.11. Este hecho muestra el interés y relevancia de los algoritmos desarrollados para la mejora de las operaciones de los satélites. Dichos algoritmos han sido presentados en varias conferencias internacionales [Sánchez-Ortiz, 2013b]T.9, [Pulido, 2014]T.7,[Grande-Olalla, 2013]T.10, [Pulido, 2014]T.5, [Sánchez-Ortiz, 2015c]T.1. ABSTRACT This document addresses methodologies for computation of the collision risk of a satellite. Two different approaches need to be considered for collision risk minimisation. On an operational basis, it is needed to perform a sieve of possible objects approaching the satellite, among all objects sharing the space with an operational satellite. As the orbits of both, satellite and the eventual collider, are not perfectly known but only estimated, the miss-encounter geometry and the actual risk of collision shall be evaluated. In the basis of the encounter geometry or the risk, an eventual manoeuvre may be required to avoid the conjunction. Those manoeuvres will be associated to a reduction in the fuel for the mission orbit maintenance, and thus, may reduce the satellite operational lifetime. Thus, avoidance manoeuvre fuel budget shall be estimated, at mission design phase, for a better estimation of mission lifetime, especially for those satellites orbiting in very populated orbital regimes. These two aspects, mission design and operational collision risk aspects, are summarised in Figure 3, and covered along this thesis. Bottom part of the figure identifies the aspects to be consider for the mission design phase (statistical characterisation of the space object population data and theory computing the mean number of events and risk reduction capability) which will define the most appropriate collision avoidance approach at mission operational phase. This part is covered in this work by starting from the theory described in [Sánchez-Ortiz, 2006]T.14 and implemented by this author in ARES tool [Sánchez-Ortiz, 2004b]T.15 provided by ESA for evaluation of collision avoidance approaches. This methodology has been now extended to account for the particular features of the available data sets in operational environment (section 4.3.3). Additionally, the formulation has been extended to allow evaluating risk computation approached when orbital uncertainty is not available (like the TLE case) and when only catastrophic collisions are subject to study (section 4.3.2.3). These improvements to the theory have been included in the new version of ESA ARES tool [Domínguez-González and Sánchez-Ortiz, 2012b]T.12 and available through [SDUP,2014]R.60. At the operation phase, the real catalogue data will be processed on a routine basis, with adequate collision risk computation algorithms to propose conjunction avoidance manoeuvre optimised for every event. The optimisation of manoeuvres in an operational basis is not approached along this document. Currently, American Two Line Element (TLE) catalogue is the only public source of data providing orbits of objects in space to identify eventual conjunction events. Additionally, Conjunction Summary Message (CSM) is provided by Joint Space Operation Center (JSpOC) when the American system identifies a possible collision among satellites and debris. Depending on the data used for collision avoidance evaluation, the conjunction avoidance approach may be different. The main features of currently available data need to be analysed (in regards to accuracy) in order to perform estimation of eventual encounters to be found along the mission lifetime. In the case of TLE, as these data is not provided with accuracy information, operational collision avoidance may be also based on statistical accuracy information as the one used in the mission design approach. This is not the case for CSM data, which includes the state vector and orbital accuracy of the two involved objects. This aspect has been analysed in detail and is depicted in the document, evaluating in statistical way the characteristics of both data sets in regards to the main aspects related to collision avoidance. Once the analysis of data set was completed, investigations on the impact of those features in the most convenient avoidance approaches have been addressed (section 5.1). This analysis is published in a peer-reviewed journal [Sánchez-Ortiz, 2015b]T.3. The analysis provides recommendations for different mission types (satellite size and orbital regime) in regards to the most appropriate collision avoidance approach for relevant risk reduction. The risk reduction capability is very much dependent on the accuracy of the catalogue utilized to identify eventual collisions. Approaches based on CSM data are recommended against the TLE based approach. Some approaches based on the maximum risk associated to envisaged encounters are demonstrated to report a very large number of events, which makes the approach not suitable for operational activities. Accepted Collision Probability Levels are recommended for the definition of the avoidance strategies for different mission types. For example for the case of a LEO satellite in the Sun-synchronous regime, the typically used ACPL value of 10-4 is not a suitable value for collision avoidance schemes based on TLE data. In this case the risk reduction capacity is almost null (due to the large uncertainties associated to TLE data sets, even for short time-to-event values). For significant reduction of risk when using TLE data, ACPL on the order of 10-6 (or lower) seems to be required, producing about 10 warnings per year and mission (if one-day ahead events are considered) or 100 warnings per year (for three-days ahead estimations). Thus, the main conclusion from these results is the lack of feasibility of TLE for a proper collision avoidance approach. On the contrary, for CSM data, and due to the better accuracy of the orbital information when compared with TLE, ACPL on the order of 10-4 allows to significantly reduce the risk. This is true for events estimated up to 3 days ahead. Even 5 days ahead events can be considered, but ACPL values down to 10-5 should be considered in such case. Even larger prediction times can be considered (7 days) for risk reduction about 90%, at the cost of larger number of warnings up to 5 events per year, when 5 days prediction allows to keep the manoeuvre rate in 2 manoeuvres per year. Dynamics of the GEO orbits is different to that in LEO, impacting on a lower increase of orbits uncertainty along time. On the contrary, uncertainties at short prediction times at this orbital regime are larger than those at LEO due to the differences in observation capabilities. Additionally, it has to be accounted that short prediction times feasible at LEO may not be appropriate for a GEO mission due to the orbital period being much larger at this regime. In the case of TLE data sets, significant reduction of risk is only achieved for small ACPL values, producing about a warning event per year if warnings are raised one day in advance to the event (too short for any reaction to be considered). Suitable ACPL values would lay in between 5•10-8 and 10-7, well below the normal values used in current operations for most of the GEO missions (TLE-based strategies for collision avoidance at this regime are not recommended). On the contrary, CSM data allows a good reduction of risk with ACPL in between 10-5 and 10-4 for short and medium prediction times. 10-5 is recommended for prediction times of five or seven days. The number of events raised for a suitable warning time of seven days would be about one in a 10-year mission. It must be noted, that these results are associated to a 2 m radius spacecraft, impact of the satellite size are also analysed within the thesis. In the future, other Space Situational Awareness Systems (SSA, ESA program) may provide additional catalogues of objects in space with the aim of reducing the risk. It is needed to investigate which are the required performances of those catalogues for allowing such risk reduction. The main performance aspects are coverage (objects included in the catalogue, mainly limited by a minimum object size derived from sensor performances) and the accuracy of the orbital data to accurately evaluate the conjunctions (derived from sensor performance in regards to object observation frequency and accuracy). The results of these investigations (section 5.2) are published in a peer-reviewed journal [Sánchez-Ortiz, 2015a]T.2. This aspect was not initially foreseen as objective of the thesis, but it shows how the theory described in the thesis, initially defined for mission design in regards to avoidance manoeuvre fuel allocation (upper part of figure 1), is extended and serves for additional purposes as dimensioning a Space Surveillance and Tracking (SST) system (bottom part of figure below). The main difference between the two approaches is the consideration of the catalogue features as part of the theory which are not modified (for the satellite mission design case) instead of being an input for the analysis (in the case of the SST design). In regards to the outputs, all the features computed by the statistical conjunction analysis are of importance for mission design (with the objective of proper global avoidance strategy definition and fuel allocation), whereas for the case of SST design, the most relevant aspects are the manoeuvre and false alarm rates (defining a reliable system) and the Risk Reduction capability (driving the effectiveness of the system). In regards to the methodology for computing the risk, the SST system shall be driven by the capacity of providing the means to avoid catastrophic conjunction events (avoiding the dramatic increase of the population), whereas the satellite mission design should consider all type of encounters, as the operator is interested on avoiding both lethal and catastrophic collisions. From the analysis of the SST features (object coverage and orbital uncertainty) for a reliable system, it is concluded that those two characteristics are to be imposed differently for the different orbital regimes, as the population level is different depending on the orbit type. Coverage values range from 5 cm for very populated LEO regime up to 100 cm in the case of GEO region. The difference on this requirement derives mainly from the relative velocity of the encounters at those regimes. Regarding the orbital knowledge of the catalogues, very accurate information is required for objects in the LEO region in order to limit the number of false alarms, whereas intermediate orbital accuracy can be considered for higher orbital regimes. In regards to the operational collision avoidance approaches, several collision risk algorithms are used for evaluation of collision risk of two pair of objects. Figure 2 provides a summary of the different collision risk algorithm cases and indicates how they are covered along this document. The typical case with high relative velocity is well covered in literature for the case of spherical objects (case A), with a large number of available algorithms, that are not analysed in detailed in this work. Only a sample case is provided in section 4.2. If complex geometries are considered (Case B), a more realistic risk evaluation can be computed. New approach for the evaluation of risk in the case of complex geometries is presented in this thesis (section 4.4.2), and it has been presented in several international conferences. The developed algorithm allows evaluating the risk for complex objects formed by a set of boxes. A dedicated Monte Carlo method has also been described (section 4.1.2.3) and implemented to allow the evaluation of the actual collisions among a large number of simulation shots. This Monte Carlo runs are considered the truth for comparison of the algorithm results (section 4.4.4). For spacecrafts that cannot be considered as spheres, the consideration of the real geometry of the objects may allow to discard events which are not real conjunctions, or estimate with larger reliability the risk associated to the event. This is of particular importance for the case of large spacecrafts as the uncertainty in positions of actual catalogues does not reach small values to make a difference for the case of objects below meter size. As the tracking systems improve and the orbits of catalogued objects are known more precisely, the importance of considering actual shapes of the objects will become more relevant. The particular case of a very large system (as a tethered satellite) is analysed in section 5.4. Additionally, if the two colliding objects have low relative velocity (and simple geometries, case C in figure above), the most common collision risk algorithms fail and adequate theories need to be applied. In this document, a low relative velocity algorithm presented in the literature [Patera, 2001]R.26 is described and evaluated (section 4.5). Evaluation through comparison with Monte Carlo approach is provided in section 4.5.2. The main conclusion of this analysis is the suitability of this algorithm for the most common encounter characteristics, and thus it is selected as adequate for collision risk estimation. Its performances are evaluated in order to characterise when it can be safely used for a large variety of encounter characteristics. In particular, it is found that the need of using dedicated algorithms depend on both the size of collision volume in the B-plane and the miss-distance uncertainty. For large uncertainties, the need of such algorithms is more relevant since for small uncertainties the encounter duration where the covariance ellipsoids intersect is smaller. Additionally, its application for the case of complex satellite geometries is assessed (case D in figure above) by integrating the developed algorithm in this thesis with Patera’s formulation for low relative velocity encounters. The results of this analysis show that the algorithm can be easily extended for collision risk estimation process suitable for complex geometry objects (section 4.5.3). The two algorithms, together with the Monte Carlo method, have been implemented in the operational tool CORAM for ESA which is used for the evaluation of collision risk of ESA operated missions, [Sánchez-Ortiz, 2013a]T.11. This fact shows the interest and relevance of the developed algorithms for improvement of satellite operations. The algorithms have been presented in several international conferences, [Sánchez-Ortiz, 2013b]T.9, [Pulido, 2014]T.7,[Grande-Olalla, 2013]T.10, [Pulido, 2014]T.5, [Sánchez-Ortiz, 2015c]T.1.

Oceanic minerals: Their origin, nature of their environment, and significance

The chemical and isotopic compositions of oceanic biogenic and authigenic minerals contain invaluable information on the evolution of seawater, hence on the history of interaction between tectonics, climate, ocean circulation, and the evolution of life. Important advances and greater understanding of (a) key minor and trace element cycles with various residence times, (b) isotopic sources and sinks and fractionation behaviors, and (c) potential diagenetic problems, as well as developments in high-precision instrumentation, recently have been achieved. These advances provided new compelling evidence that neither gradualism nor uniformitarianism can explain many of the new important discoveries obtained from the chemistry and isotopic compositions of oceanic minerals. Presently, the best-developed geochemical proxies in biogenic carbonates are 18O/16O and Sr/Ca ratios (possibly Mg/Ca) for temperature; 87Sr/86Sr for input sources, Cd/Ca and Ba/Ca ratios for phosphate and alkalinity concentrations, respectively, thus also for ocean circulation; 13C/12C for ocean productivity; B isotopes for seawater pH;, U, Th isotopes, and 14C for dating; and Sr and Mn concentrations for diagenesis. The oceanic authigenic minerals most widely used for chemical paleoceanography are barite, evaporite sulfates, and hydrogenous ferromanganese nodules. Marine barite is an effective alternative monitor of seawater 87Sr/86Sr, especially where carbonates are diagenetically altered or absent. It also provides a high-resolution record of seawater sulfate S isotopes, (evaporite sulfates only carry an episodic record), with new insights on factors affecting the S and C cycles and atmospheric oxygen. High-resolution studies of Sr, Nd, and Pb isotopes of well-dated ferromanganese nodules contain invaluable records on climate driven changes in oceanic circulation.

Augmented significance routines for Illiac IV /

Includes bibliographies (p. 18).

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

Compositional semantics of dataflow networks with query-driven communication of exact values

We develop and study the concept of dataflow process networks as used for exampleby Kahn to suit exact computation over data types related to real numbers, such as continuous functions and geometrical solids. Furthermore, we consider communicating these exact objectsamong processes using protocols of a query-answer nature as introduced in our earlier work. This enables processes to provide valid approximations with certain accuracy and focusing on certainlocality as demanded by the receiving processes through queries. We define domain-theoretical denotational semantics of our networks in two ways: (1) directly, i. e. by viewing the whole network as a composite process and applying the process semantics introduced in our earlier work; and (2) compositionally, i. e. by a fixed-point construction similarto that used by Kahn from the denotational semantics of individual processes in the network. The direct semantics closely corresponds to the operational semantics of the network (i. e. it iscorrect) but very difficult to study for concrete networks. The compositional semantics enablescompositional analysis of concrete networks, assuming it is correct. We prove that the compositional semantics is a safe approximation of the direct semantics. Wealso provide a method that can be used in many cases to establish that the two semantics fully coincide, i. e. safety is not achieved through inactivity or meaningless answers. The results are extended to cover recursively-defined infinite networks as well as nested finitenetworks. A robust prototype implementation of our model is available.

A knowledge driven approach towards the validation of externally acquired traceability datasets in supply chain business processes

The sharing of near real-time traceability knowledge in supply chains plays a central role in coordinating business operations and is a key driver for their success. However before traceability datasets received from external partners can be integrated with datasets generated internally within an organisation, they need to be validated against information recorded for the physical goods received as well as against bespoke rules defined to ensure uniformity, consistency and completeness within the supply chain. In this paper, we present a knowledge driven framework for the runtime validation of critical constraints on incoming traceability datasets encapuslated as EPCIS event-based linked pedigrees. Our constraints are defined using SPARQL queries and SPIN rules. We present a novel validation architecture based on the integration of Apache Storm framework for real time, distributed computation with popular Semantic Web/Linked data libraries and exemplify our methodology on an abstraction of the pharmaceutical supply chain.

Candidate knowledge? Exploring epistemic claims in scientific writing:a corpus-driven approach

In this article I argue that the study of the linguistic aspects of epistemology has become unhelpfully focused on the corpus-based study of hedging and that a corpus-driven approach can help to improve upon this. Through focusing on a corpus of texts from one discourse community (that of genetics) and identifying frequent tri-lexical clusters containing highly frequent lexical items identified as keywords, I undertake an inductive analysis identifying patterns of epistemic significance. Several of these patterns are shown to be hedging devices and the whole corpus frequencies of the most salient of these, candidate and putative, are then compared to the whole corpus frequencies for comparable wordforms and clusters of epistemic significance. Finally I interviewed a ‘friendly geneticist’ in order to check my interpretation of some of the terms used and to get an expert interpretation of the overall findings. In summary I argue that the highly unexpected patterns of hedging found in genetics demonstrate the value of adopting a corpus-driven approach and constitute an advance in our current understanding of how to approach the relationship between language and epistemology.

Strontium isotopes and sedimentology of a marine Triassic succession (upper Ladinian) of the westernmost Tethys, Spain

Chemical Stratigraphy, or the study of the variation of chemical elements within sedimentary sequences, has gradually become an experienced tool in the research and correlation of global geologic events. In this paper 87Sr/ 86Sr ratios of the Triassic marine carbonates (Muschelkalk facies) of southeast Iberian Ranges, Iberian Peninsula, are presented and the representative Sr-isotopic curve constructed for the upper Ladinian interval. The studied stratigraphic succession is 102 meters thick, continuous, and well preserved. Previous paleontological data from macro and micro, ammonites, bivalves, foraminifera, conodonts and palynological assemblages, suggest a Fassanian-Longobardian age (Late Ladinian). Although diagenetic minerals are present in small amounts, the elemental data content of bulk carbonate samples, especially Sr contents, show a major variation that probably reflects palaeoenvironmental changes. The 87Sr/86Sr ratios curve shows a rise from 0.707649 near the base of the section to 0.707741 and then declines rapidly to 0.707624, with a final values rise up to 0.70787 in the upper part. The data up to meter 80 in the studied succession is broadly concurrent with 87Sr/86Sr ratios of sequences of similar age and complements these data. Moreover, the sequence stratigraphic framework and its key surfaces, which are difficult to be recognised just based in the facies analysis, are characterised by combining variations of the Ca, Mg, Mn, Sr and CaCO3 contents

On the Incorporation of Psychologically-Driven 'Music' Preference Models for Music Recommendation

There are hundreds of millions of songs available to the public, necessitating the use of music recommendation systems to discover new music. Currently, such systems account for only the quantitative musical elements of songs, failing to consider aspects of human perception of music and alienating the listener’s individual preferences from recommendations. Our research investigated the relationships between perceptual elements of music, represented by the MUSIC model, with computational musical features generated through The Echo Nest, to determine how a psychological representation of music preference can be incorporated into recommendation systems to embody an individual’s music preferences. Our resultant model facilitates computation of MUSIC factors using The Echo Nest features, and can potentially be integrated into recommendation systems for improved performance.

Discovery driven analysis on semi-structured text data

Discovery Driven Analysis (DDA) is a common feature of OLAP technology to analyze structured data. In essence, DDA helps analysts to discover anomalous data by highlighting 'unexpected' values in the OLAP cube. By giving indications to the analyst on what dimensions to explore, DDA speeds up the process of discovering anomalies and their causes. However, Discovery Driven Analysis (and OLAP in general) is only applicable on structured data, such as records in databases. We propose a system to extend DDA technology to semi-structured text documents, that is, text documents with a few structured data. Our system pipeline consists of two stages: first, the text part of each document is structured around user specified dimensions, using semi-PLSA algorithm; then, we adapt DDA to these fully structured documents, thus enabling DDA on text documents. We present some applications of this system in OLAP analysis and show how scalability issues are solved. Results show that our system can handle reasonable datasets of documents, in real time, without any need for pre-computation.

Two-dimensional Stokes flow driven by elliptical paddles

A fast and accurate numerical technique is developed for solving the biharmonic equation in a multiply connected domain, in two dimensions. We apply the technique to the computation of slow viscous flow (Stokes flow) driven by multiple stirring rods. Previously, the technique has been restricted to stirring rods of circular cross section; we show here how the prior method fails for noncircular rods and how it may be adapted to accommodate general rod cross sections, provided only that for each there exists a conformal mapping to a circle. Corresponding simulations of the flow are described, and their stirring properties and energy requirements are discussed briefly. In particular the method allows an accurate calculation of the flow when flat paddles are used to stir a fluid chaotically.

SECURITY, PRIVACY AND APPLICATIONS IN VEHICULAR AD HOC NETWORKS

With wireless vehicular communications, Vehicular Ad Hoc Networks (VANETs) enable numerous applications to enhance traffic safety, traffic efficiency, and driving experience. However, VANETs also impose severe security and privacy challenges which need to be thoroughly investigated. In this dissertation, we enhance the security, privacy, and applications of VANETs, by 1) designing application-driven security and privacy solutions for VANETs, and 2) designing appealing VANET applications with proper security and privacy assurance. First, the security and privacy challenges of VANETs with most application significance are identified and thoroughly investigated. With both theoretical novelty and realistic considerations, these security and privacy schemes are especially appealing to VANETs. Specifically, multi-hop communications in VANETs suffer from packet dropping, packet tampering, and communication failures which have not been satisfyingly tackled in literature. Thus, a lightweight reliable and faithful data packet relaying framework (LEAPER) is proposed to ensure reliable and trustworthy multi-hop communications by enhancing the cooperation of neighboring nodes. Message verification, including both content and signature verification, generally is computation-extensive and incurs severe scalability issues to each node. The resource-aware message verification (RAMV) scheme is proposed to ensure resource-aware, secure, and application-friendly message verification in VANETs. On the other hand, to make VANETs acceptable to the privacy-sensitive users, the identity and location privacy of each node should be properly protected. To this end, a joint privacy and reputation assurance (JPRA) scheme is proposed to synergistically support privacy protection and reputation management by reconciling their inherent conflicting requirements. Besides, the privacy implications of short-time certificates are thoroughly investigated in a short-time certificates-based privacy protection (STCP2) scheme, to make privacy protection in VANETs feasible with short-time certificates. Secondly, three novel solutions, namely VANET-based ambient ad dissemination (VAAD), general-purpose automatic survey (GPAS), and VehicleView, are proposed to support the appealing value-added applications based on VANETs. These solutions all follow practical application models, and an incentive-centered architecture is proposed for each solution to balance the conflicting requirements of the involved entities. Besides, the critical security and privacy challenges of these applications are investigated and addressed with novel solutions. Thus, with proper security and privacy assurance, these solutions show great application significance and economic potentials to VANETs. Thus, by enhancing the security, privacy, and applications of VANETs, this dissertation fills the gap between the existing theoretic research and the realistic implementation of VANETs, facilitating the realistic deployment of VANETs.