Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Microalgal CO2 Sequestering - Modeling Microalgae Production Costs

Microalgae CO2 sequestering facilities might become an industrial reality if microalgae biomass could be produced at cost below $500.00 t-1. We develop a model for estimation of total production costs of microalgae as a function of known production-specific expenses, and incorporate into the model the effects of uncontrollable factors which affect known production-specific expenses. Random fluctuations were intentionally incorporated into the model, consequently into generated cost/technology scenarios, because each and every logically interconnected equipment/operation that is used in design/construction/operation/maintenance of a production process is inevitably subject to random cost/price fluctuations which can neither be eliminated nor a priori controlled. A total of 152 costs/technology scenarios were evaluated to find forty four scenarios in which Predicted Total Production Costs of Microalgae (PTPCM) was in the range $200 to $500 t-1 ha-1 y-1. An additional 24 scenarios were found with PTCPM in the range of $102 to $200 t-1 ha-1 y-1. These findings suggest that microalgae CO2 sequestering and the production of commercial compounds from microalgal biomass can be economically viable venture even today when microalgae production technology is still far from its optimum.

Population genetic and dispersal modeling data for Bathymodiolus mussels from the Mid-Atlantic Ridge

The zip folder comprises a text file and a gzipped tar archive. 1) The text file contains individual genotype data for 90 SNPs, 9 microsatellites and the mitochondrial ND4 gene that were determined in deep-sea hydrothermal vent mussels from the Mid-Atlantic Ridge (genus Bathymodiolus). Mussel specimens are grouped according to the population (pop)/location from which they have been sampled (first column). The remaining columns contain the respective allele/haplotype codes for the different genetic loci (names in the header line). The data file is in CONVERT format and can be directly transformed into different input files for population genetic statistics. 2) The tar archive contains NetCDF files with larval dispersal probabilities for simulated annual larval releases between 1998 and 2007. For each simulated vent location (Menez Gwen, Lucky Strike, Rainbow, Vent 1-10) two NetCDF files are given, one for an assumed pelagic larval duration of 1 year and the other one for an assumed pelagic larval duration of 6 months (6m).

The "Catching up" Process of Manufacturing in East Asia

This paper examines the "catching up" process of manufacturing in East Asia within the framework of North and South location. Results of this study indicate that latecomers of the ASEAN Four and China have advanced the "catching up" process. At the same time, second-runners of the Asian NIES have more extensively increased their "catching up" with Japan. Most "catching up" was realized in a very short period in the 1990s, and the advancement of the "catching up" process has moved into various industries from nondurable products to light machinery products. However, it has not yet advanced in heavy machinery such as in the industrial machinery and machine tool industries.

The location of manufacturing firms and imperfect information in transport market

It is well know that transport charges are not symmetric: fronthaul and backhaul costs on a route may differ, because they are affected by the distribution of economic acitivities. This paper develops a two-regional general equilibrium model in which transport costs are determined endogenously as a result of a search and matching process. It is shown that economies or diseconomies of transport density emerge, depending on the search costs of transport firms and the relative importance of the possibility of backhaul transportation. It is found that the symmetry of the distribution of economic activity may break owing to economies of transport density when the additional search costs are small enough.

Relaciones entre los usos del suelo, las infraestructuras y la planificación: incidencia de la red viaria y el planeamiento en la aparición del terciario para el caso de la N-VI

Esta tesis examina el papel de la red viaria y el planeamiento urbanístico en la localización de las actividades terciarias. A partir de los años sesenta se produce una modificación de los patrones de comportamiento espacial de las actividades productivas. En la raíz de estos cambios está los procesos de globalización e internacionalización de la economía y un importante aumento de la utilización vehículos privados. Todo ello da lugar a una preocupación entre los profesionales por la identificación de variables en esa organización espacial, y por la búsqueda de modelos que mejorasen las condiciones de competitividad en el entramado urbano, reclamado también la formulación de conceptos diferentes, capaces de entender los cambios territoriales de la reestructuración permanente en que viven las economías capitalistas avanzadas. En este marco, hay un aumento importante de las actividades terciarias o proceso de terciarización; que es el principio basilar para la suburbanización de este sector. Consiste, en buena medida, en unas necesidades de descentralización y dispersión de las actividades terciarias por todo el territorio, con demandas de nuevos espacios para todo tipo de actividades empresariales. Se va así generando un espacio urbano complejo, con nuevas actividades, distintas de la residencial, y con tipologías edificatorias diferentes: centros comerciales, hipermercados, zocos o edificios de empresas dedicadas a servicios avanzados y altamente cualificados. Adquiere, por tanto, un fuerte protagonismo los espacios periféricos de las grandes ciudades. En la transformación de este territorio interviene el planeamiento urbanístico porque prevé la ocupación del suelo y la forma de uso. Y también la carretera considerada clave en el desarrollo histórico de la ciudad. Consecuentemente, se impulsan una plétora de nuevas líneas de investigación y nuevas formas de aproximación al estudio de las relaciones entre las infraestructuras viarias y los usos del suelo. El interés del proyecto de investigación es, por todo ello, estudiar en que medida la localización del terciario depende del planeamiento urbano y de las variaciones en la red viaria. Es decir, la hipótesis de este trabajo se puede enunciar diciendo que: en la aparición del terciario inciden dos variables, el planeamiento urbanístico y la red viaria; lógicamente siendo consciente de la dificultad intrínseca de separar algún parámetro y sus relaciones de un sistema funcional urbano. Centrando este enfoque sobre el caso particular del corredor de la carretera de La Coruña (N-VI) situado en el oeste de la Comunidad de Madrid. Es un ámbito suburbano que comprende los términos municipales de Las Rozas y Majadahonda, un segmento del municipio de Madrid (abarca los barrios de Aravaca, el Plantío y Valdemarín, y una pequeña superficie de la Casa de Campo, Ciudad Universitaria y El Pardo), y la mitad septentrional del municipio de Pozuelo de Alarcón. La conclusión general a la que se ha llegado es que se trata de un fenómeno complejo, en el que se detecta que: A) La aprobación de un nuevo Plan Urbanístico no supone un cambio inmediato en la evolución cuantitativa de la implantación de actividades terciarias en edificio exclusivo en el área de estudio. B) Se evidencia una relación directa entre la implantación de una nueva infraestructura de transporte o modificación de algún elemento importante y el crecimiento de la localización de actividades terciarias. C) Resulta difícil verificar que cuando confluyen mejoras o nuevas construcciones en la red viaria y una estrategia en el planeamiento dirigida a la ordenación e intervención del espacio terciario, el número de edificios terciarios aumente. ABSTRACT This thesis examines the role of road networks and urban planning in the location of tertiary activities. Since the sixties there is a modification of spatial behavior patterns of production activities. At the root of these changes is the process of globalization and internationalization of the economy and a significant increase in private car use. This leads to a concern among professionals in the identification of variables in the spatial organization, and the search for models that would improve the competitive conditions in the urban framework, also called for the formulation of different concepts, able to understand the changes territorial restructuring that live permanently in the advanced capitalist economies. In this context, there is a significant increase in tertiary activities or process outsourcing, which is the beginning basilar to the suburbanization of the sector. It consists, in large part, on the Needs of decentralization and dispersal of tertiary activities throughout the territory, demands for new spaces for all types of business activities. It is thus generating a complex urban area, with new activities, other than residential and with different building typologies: shopping malls, hypermarkets, souks and buildings of companies engaged in advanced and highly skilled services. Thus takes strong role peripheral areas of big cities. In the transformation of this region is involved in providing for urban planning land use and how to use. And the road is considered key in the historical development of the city. Consequently, they are promoting a plethora of new research and new ways of approaching the study of the relationship between road infrastructure and land use. The interest of the research project is, for all that, consider to what extent depends on the location of tertiary urban planning and changes in the road network. That is, the hypothesis of this work can be stated by saying that: the emergence of two variables affecting tertiary, urban planning and road network, of course being aware of the inherent difficulty of separating any parameters and functional relationships of an urban. Approach focusing on the particular case of the road corridor from La Coruña (N-VI) located in the west of Madrid. It is a suburban area comprising the municipalities of Las Rozas and Majadahonda, a segment of the city of Madrid (covering the districts of Aravaca, the planting and Valdemarín, and a small area of the Casa de Campo, Ciudad Universitaria and El Pardo) , and the northern half of the town of Pozuelo de Alarcón. The general conclusion has been reached is that this is a complex phenomenon, which is detected: A) The approval of a new Urban Plan is not an immediate change in the quantitative evolution of the implementation of tertiary activities in exclusive building in the study area. B) It shows a direct relationship between the introduction of a new transport infrastructure or amendment to an important and growing element of the location of tertiary activities. C) It is difficult to verify that when improvements or new construction come together in the road network and planning a strategy aimed at the management and intervention of third space, the number of commercial buildings increases.

Improving Speech Interaction in Vehicles Using Context-Aware Information through A SCXML Framework

Speech Technologies can provide important benefits for the development of more usable and safe in-vehicle human-machine interactive systems (HMIs). However mainly due robustness issues, the use of spoken interaction can entail important distractions to the driver. In this challenging scenario, while speech technologies are evolving, further research is necessary to explore how they can be complemented with both other modalities (multimodality) and information from the increasing number of available sensors (context-awareness). The perceived quality of speech technologies can significantly be increased by implementing such policies, which simply try to make the best use of all the available resources; and the in vehicle scenario is an excellent test-bed for this kind of initiatives. In this contribution we propose an event-based HMI design framework which combines context modelling and multimodal interaction using a W3C XML language known as SCXML. SCXML provides a general process control mechanism that is being considered by W3C to improve both voice interaction (VoiceXML) and multimodal interaction (MMI). In our approach we try to anticipate and extend these initiatives presenting a flexible SCXML-based approach for the design of a wide range of multimodal context-aware HMI in-vehicle interfaces. The proposed framework for HMI design and specification has been implemented in an automotive OSGi service platform, and it is being used and tested in the Spanish research project MARTA for the development of several in-vehicle interactive applications.

Interactive Graphic Simulation: An Advanced Methodology to Improve the Teaching-Learning Process in Nuclear Engineering Education and Training

Nowadays, computer simulators are becoming basic tools for education and training in many engineering fields. In the nuclear industry, the role of simulation for training of operators of nuclear power plants is also recognized of the utmost relevance. As an example, the International Atomic Energy Agency sponsors the development of nuclear reactor simulators for education, and arranges the supply of such simulation programs. Aware of this, in 2008 Gas Natural Fenosa, a Spanish gas and electric utility that owns and operate nuclear power plants and promotes university education in the nuclear technology field, provided the Department of Nuclear Engineering of Universidad Politécnica de Madrid with the Interactive Graphic Simulator (IGS) of “José Cabrera” (Zorita) nuclear power plant, an industrial facility whose commercial operation ceased definitively in April 2006. It is a state-of-the-art full-scope real-time simulator that was used for training and qualification of the operators of the plant control room, as well as to understand and analyses the plant dynamics, and to develop, qualify and validate its emergency operating procedures.

A Video-Aware FEC-Based Unequal Loss Protection Scheme for RTP Video Streaming

A video-aware unequal loss protection (ULP) system for protecting RTP video streaming in bursty packet loss networks is proposed. Just considering the relevance of the frame, the state of the channel and the bitrate constraints of the protection bitstream, our algorithm selects in real time the most suitable frames to be protected through forward error correction (FEC) techniques. It benefits from a wise RTP encapsulation that allows working at a frame level without requiring any further process than that of parsing RTP headers, so it is perfectly suitable to be included in commercial transmitters. The simulation results show how our proposed ULP technique outperforms non-smart schemes.

Application of the Extended Kalman filter to fuzzy modeling: Algorithms and practical implementation

Modeling phase is fundamental both in the analysis process of a dynamic system and the design of a control system. If this phase is in-line is even more critical and the only information of the system comes from input/output data. Some adaptation algorithms for fuzzy system based on extended Kalman filter are presented in this paper, which allows obtaining accurate models without renounce the computational efficiency that characterizes the Kalman filter, and allows its implementation in-line with the process

Using SCXML to integrate semantic sensor information into context-aware user interfaces

This paper describes a novel architecture to introduce automatic annotation and processing of semantic sensor data within context-aware applications. Based on the well-known state-charts technologies, and represented using W3C SCXML language combined with Semantic Web technologies, our architecture is able to provide enriched higher-level semantic representations of user’s context. This capability to detect and model relevant user situations allows a seamless modeling of the actual interaction situation, which can be integrated during the design of multimodal user interfaces (also based on SCXML) for them to be adequately adapted. Therefore, the final result of this contribution can be described as a flexible context-aware SCXML-based architecture, suitable for both designing a wide range of multimodal context-aware user interfaces, and implementing the automatic enrichment of sensor data, making it available to the entire Semantic Sensor Web

Ecient Inference-aware RDB2RDF Query Rewriting

RDB2RDF systems generate RDF from relational databases, operating in two dierent manners: materializing the database content into RDF or acting as virtual RDF datastores that transform SPARQL queries into SQL. In the former, inferences on the RDF data (taking into account the ontologies that they are related to) are normally done by the RDF triple store where the RDF data is materialised and hence the results of the query answering process depend on the store. In the latter, existing RDB2RDF systems do not normally perform such inferences at query time. This paper shows how the algorithm used in the REQUIEM system, focused on handling run-time inferences for query answering, can be adapted to handle such inferences for query answering in combination with RDB2RDF systems.

Ecient Inference-aware RDB2RDF Query Rewriting

RDB2RDF systems generate RDF from relational databases, operating in two di�erent manners: materializing the database content into RDF or acting as virtual RDF datastores that transform SPARQL queries into SQL. In the former, inferences on the RDF data (taking into account the ontologies that they are related to) are normally done by the RDF triple store where the RDF data is materialised and hence the results of the query answering process depend on the store. In the latter, existing RDB2RDF systems do not normally perform such inferences at query time. This paper shows how the algorithm used in the REQUIEM system, focused on handling run-time inferences for query answering, can be adapted to handle such inferences for query answering in combination with RDB2RDF systems.

Generating context-aware recommendations using banking data in a mobile recommender system

The increasing adoption of smartphones by the society has created a new area of research in recommender systems. This new domain is based on using location and context-awareness to provide personalization. This paper describes a model to generate context-aware recommendations for mobile recommender systems using banking data in order to recommend places where the bank customers have previously spent their money. In this work we have used real data provided by a well know Spanish bank. The mobile prototype deployed in the bank Labs environment was evaluated in a survey among 100 users with good results regarding usefulness and effectiveness. The results also showed that test users had a high confidence in a recommender system based on real banking data.

Towards architectural foundations for cognitive self-aware systems

In this talk we address a proposal concerning a methodology for extracting universal, domain neutral, architectural design patterns from the analysis of biological cognition. This will render a set of design principles and design patterns oriented towards the construction of better machines. Bio- inspiration cannot be a one step process if we we are going to to build robust, dependable autonomous agents; we must build solid theories first, departing from natural systems, and supporting our designs of artificial ones.