DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

MRI texture analysis as means for addressing rehydration and milk diffusion of cereals

Cereals microstructure is one of the primary quality attributes of cereals. Cereals rehydration and milk diffusion depends on such microstructure and thus, the crispiness and the texture, which will make it more palatable for the final consumer. Magnetic Resonance Imaging (MRI) is a very powerful topographic tool since acquisition parameter leads to a wide possibility for identifying textures, structures and liquids mobility. It is suited for non-invasive imaging of water and fats. Rehydration and diffusion cereals processes were measured by MRI at different times and using two different kinds of milk, varying their fat level. Several images were obtained. A combination of textural analysis (based on the analysis of histograms) and segmentation methods (in order to understand the rehydration level of each variety of cereals) were performed. According to the rehydration level, no advisable clustering behavior was found. Nevertheless, some differences were noticeable between the coating, the type of milk and the variety of cereals

An Analysis of Next Generation Access Networks Deployment in rural areas

Next generation access networks (NGAN) will support a renewed electronic communication market where main opportunities lie in the provision of ubiquitous broadband connectivity, applications and content. From their deployment it is expected a wealth of innovations. Within this framework, the project reviews the variety of NGAN deployment options available for rural environments, derives a simple method for approximate cost calculations, and then discusses and compares the results obtained. Data for Spain are used for practical calculations, but the model is applicable with minor modifications to most of the rural areas of European countries. The final part of the paper is devoted to review the techno-economic implications of a network deployment in a rural environment as well as the adequacy and possible developments of the regulatory framework involved

Dynamic analysis of road vehicle-bridge systems under turbulent wind by means of Finite Element Models

When an automobile passes over a bridge dynamic effects are produced in vehicle and structure. In addition, the bridge itself moves when exposed to the wind inducing dynamic effects on the vehicle that have to be considered. The main objective of this work is to understand the influence of the different parameters concerning the vehicle, the bridge, the road roughness or the wind in the comfort and safety of the vehicles when crossing bridges. Non linear finite element models are used for structures and multibody dynamic models are employed for vehicles. The interaction between the vehicle and the bridge is considered by contact methods. Road roughness is described by the power spectral density (PSD) proposed by the ISO 8608. To consider that the profiles under right and left wheels are different but not independent, the hypotheses of homogeneity and isotropy are assumed. To generate the wind velocity history along the road the Sandia method is employed. The global problem is solved by means of the finite element method. First the methodology for modelling the interaction is verified in a benchmark. Following, the case of a vehicle running along a rigid road and subjected to the action of the turbulent wind is analyzed and the road roughness is incorporated in a following step. Finally the flexibility of the bridge is added to the model by making the vehicle run over the structure. The application of this methodology will allow to understand the influence of the different parameters in the comfort and safety of road vehicles crossing wind exposed bridges. Those results will help to recommend measures to make the traffic over bridges more reliable without affecting the structural integrity of the viaduct

Signal analysis and feature generation for pattern identification of partial discharges in high-voltage equipment

This paper proposes a method for the identification of different partial discharges (PDs) sources through the analysis of a collection of PD signals acquired with a PD measurement system. This method, robust and sensitive enough to cope with noisy data and external interferences, combines the characterization of each signal from the collection, with a clustering procedure, the CLARA algorithm. Several features are proposed for the characterization of the signals, being the wavelet variances, the frequency estimated with the Prony method, and the energy, the most relevant for the performance of the clustering procedure. The result of the unsupervised classification is a set of clusters each containing those signals which are more similar to each other than to those in other clusters. The analysis of the classification results permits both the identification of different PD sources and the discrimination between original PD signals, reflections, noise and external interferences. The methods and graphical tools detailed in this paper have been coded and published as a contributed package of the R environment under a GNU/GPL license.

Power system stability of a small sized isolated network supplied by a combined wind-pumped storage generation system: a case study in the Canary Islands

Massive integration of renewable energy sources in electrical power systems of remote islands is a subject of current interest. The increasing cost of fossil fuels, transport costs to isolated sites and environmental concerns constitute a serious drawback to the use of conventional fossil fuel plants. In a weak electrical grid, as it is typical on an island, if a large amount of conventional generation is substituted by renewable energy sources, power system safety and stability can be compromised, in the case of large grid disturbances. In this work, a model for transient stability analysis of an isolated electrical grid exclusively fed from a combination of renewable energy sources has been studied. This new generation model will be installed in El Hierro Island, in Spain. Additionally, an operation strategy to coordinate the generation units (wind, hydro) is also established. Attention is given to the assessment of inertial energy and reactive current to guarantee power system stability against large disturbances. The effectiveness of the proposed strategy is shown by means of simulation results.

Conductance interaction identification by means of Boltzmann distribution and mutual information analysis in conductance-based neuron models

Conductance interaction identification by means of Boltzmann distribution and mutual information analysis in conductance-based neuron models.

Physical characterization of laser interaction and shock generation in laser processing: coupled theoretical-experimental analysis

Outline: • Introduction • Fundamental Physics of the Laser-Plasma Interaction in Laser Shock Processing • Theoretical/Computational Model Description • Some Results. Analysis of Interaction Parameters • Experimental Validation. Diagnosis Setup • Discussion and Outlook

Common motifs in scientific workflows: An empirical analysis

While workflow technology has gained momentum in the last decade as a means for specifying and enacting computational experiments in modern science, reusing and repurposing existing workflows to build new scientific experiments is still a daunting task. This is partly due to the difficulty that scientists experience when attempting to understand existing workflows, which contain several data preparation and adaptation steps in addition to the scientifically significant analysis steps. One way to tackle the understandability problem is through providing abstractions that give a high-level view of activities undertaken within workflows. As a first step towards abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna and Wings systems. Our analysis has resulted in a set of scientific workflow motifs that outline i) the kinds of data intensive activities that are observed in workflows (data oriented motifs), and ii) the different manners in which activities are implemented within workflows (workflow oriented motifs). These motifs can be useful to inform workflow designers on the good and bad practices for workflow development, to inform the design of automated tools for the generation of workflow abstractions, etc.

Technical evaluation of a third generation optical pose tracker for motion analysis and image-guided surgery

Laparoscopic instrument tracking systems are an essential component in image-guided interventions and offer new possibilities to improve and automate objective assessment methods of surgical skills. In this study we present our system design to apply a third generation optical pose tracker (Micron- Tracker®) to laparoscopic practice. A technical evaluation of this design is performed in order to analyze its accuracy in computing the laparoscopic instrument tip position. Results show a stable fluctuation error over the entire analyzed workspace. The relative position errors are 1.776±1.675 mm, 1.817±1.762 mm, 1.854±1.740 mm, 2.455±2.164 mm, 2.545±2.496 mm, 2.764±2.342 mm, 2.512±2.493 mm for distances of 50, 100, 150, 200, 250, 300, and 350 mm, respectively. The accumulated distance error increases with the measured distance. The instrument inclination covered by the system is high, from 90 to 7.5 degrees. The system reports a low positional accuracy for the instrument tip.

Common motifs in scientific workflows: An empirical analysis

Workflow technology continues to play an important role as a means for specifying and enacting computational experiments in modern science. Reusing and re-purposing workflows allow scientists to do new experiments faster, since the workflows capture useful expertise from others. As workflow libraries grow, scientists face the challenge of finding workflows appropriate for their task, understanding what each workflow does, and reusing relevant portions of a given workflow.We believe that workflows would be easier to understand and reuse if high-level views (abstractions) of their activities were available in workflow libraries. As a first step towards obtaining these abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna, Wings, Galaxy and Vistrails. Our analysis has resulted in a set of scientific workflow motifs that outline (i) the kinds of data-intensive activities that are observed in workflows (Data-Operation motifs), and (ii) the different manners in which activities are implemented within workflows (Workflow-Oriented motifs). These motifs are helpful to identify the functionality of the steps in a given workflow, to develop best practices for workflow design, and to develop approaches for automated generation of workflow abstractions.

Simulation, Design and Analysis of Air-Breathing Combined-Cycle Engines for High Speed Propulsion

Desde la aparición del turborreactor, el motor aeróbico con turbomaquinaria ha demostrado unas prestaciones excepcionales en los regímenes subsónico y supersónico bajo. No obstante, la operación a velocidades superiores requiere sistemas más complejos y pesados, lo cual ha imposibilitado la ejecución de estos conceptos. Los recientes avances tecnológicos, especialmente en materiales ligeros, han restablecido el interés por los motores de ciclo combinado. La simulación numérica de estos nuevos conceptos es esencial para estimar las prestaciones de la planta propulsiva, así como para abordar las dificultades de integración entre célula y motor durante las primeras etapas de diseño. Al mismo tiempo, la evaluación de estos extraordinarios motores requiere una metodología de análisis distinta. La tesis doctoral versa sobre el diseño y el análisis de los mencionados conceptos propulsivos mediante el modelado numérico y la simulación dinámica con herramientas de vanguardia. Las distintas arquitecturas presentadas por los ciclos combinados basados en sendos turborreactor y motor cohete, así como los diversos sistemas comprendidos en cada uno de ellos, hacen necesario establecer una referencia común para su evaluación. Es más, la tendencia actual hacia aeronaves "más eléctricas" requiere una nueva métrica para juzgar la aptitud de un proceso de generación de empuje en el que coexisten diversas formas de energía. A este respecto, la combinación del Primer y Segundo Principios define, en un marco de referencia absoluto, la calidad de la trasferencia de energía entre los diferentes sistemas. Esta idea, que se ha estado empleando desde hace mucho tiempo en el análisis de plantas de potencia terrestres, ha sido extendida para relacionar la misión de la aeronave con la ineficiencia de cada proceso involucrado en la generación de empuje. La metodología se ilustra mediante el estudio del motor de ciclo combinado variable de una aeronave para el crucero a Mach 5. El diseño de un acelerador de ciclo combinado basado en el turborreactor sirve para subrayar la importancia de la integración del motor y la célula. El diseño está limitado por la trayectoria ascensional y el espacio disponible en la aeronave de crucero supersónico. Posteriormente se calculan las prestaciones instaladas de la planta propulsiva en función de la velocidad y la altitud de vuelo y los parámetros de control del motor: relación de compresión, relación aire/combustible y área de garganta. ABSTRACT Since the advent of the turbojet, the air-breathing engine with rotating machinery has demonstrated exceptional performance in the subsonic and low supersonic regimes. However, the operation at higher speeds requires further system complexity and weight, which so far has impeded the realization of these concepts. Recent technology developments, especially in lightweight materials, have restored the interest towards combined-cycle engines. The numerical simulation of these new concepts is essential at the early design stages to compute a first estimate of the engine performance in addition to addressing airframe-engine integration issues. In parallel, a different analysis methodology is required to evaluate these unconventional engines. The doctoral thesis concerns the design and analysis of the aforementioned engine concepts by means of numerical modeling and dynamic simulation with state-of-the-art tools. A common reference is needed to evaluate the different architectures of the turbine and the rocket-based combined-cycle engines as well as the various systems within each one of them. Furthermore, the actual trend towards more electric aircraft necessitates a common metric to judge the suitability of a thrust generation process where different forms of energy coexist. In line with this, the combination of the First and the Second Laws yields the quality of the energy being transferred between the systems on an absolute reference frame. This idea, which has been since long applied to the analysis of on-ground power plants, was extended here to relate the aircraft mission with the inefficiency of every process related to the thrust generation. The methodology is illustrated with the study of a variable- combined-cycle engine for a Mach 5 cruise aircraft. The design of a turbine-based combined-cycle booster serves to highlight the importance of the engine-airframe integration. The design is constrained by the ascent trajectory and the allocated space in the supersonic cruise aircraft. The installed performance of the propulsive plant is then computed as a function of the flight speed and altitude and the engine control parameters: pressure ratio, air-to-fuel ratio and throat area.

Signal analysis and feature generation for pattern identification of partial discharges in high-voltage equipment

This paper proposes a method for the identification of different partial discharges (PDs) sources through the analysis of a collection of PD signals acquired with a PD measurement system. This method, robust and sensitive enough to cope with noisy data and external interferences, combines the characterization of each signal from the collection, with a clustering procedure, the CLARA algorithm. Several features are proposed for the characterization of the signals, being the wavelet variances, the frequency estimated with the Prony method, and the energy, the most relevant for the performance of the clustering procedure. The result of the unsupervised classification is a set of clusters each containing those signals which are more similar to each other than to those in other clusters. The analysis of the classification results permits both the identification of different PD sources and the discrimination between original PD signals, reflections, noise and external interferences. The methods and graphical tools detailed in this paper have been coded and published as a contributed package of the R environment under a GNU/GPL license.

Analysis of plate bending by means of high order finite hyperelements

The possibilities and limitations of high order hyperelements in plate bending analysis are discussed. Explicit shape functions for some types of triangular elements are given. These elements are applied to simple cases to assess their computational efficiency.

Experimental analysis of energy savings and hygrothermal conditions improvement by means of air curtaines in stores with intensive pedestrian traffic

Current worldwide building legislation requirements aim to the design and construction of technical services that reduce energy consumption and improve indoor hygrothermal conditions. The retail sector in Spain, with a lot of outdated technical systems, demands energy conservation measures in order to reduce the increasingly electrical consumption for cooling. Climatic separation with modern air curtains and advanced hygrothermal control systems enables energy savings and can keep suitable indoor air temperature and humidity of stores with intense pedestrian traffic, especially when located in hot humid climates. As stated in the article, the energy savings in commercial buildings with these systems exceeds 30%