Inexact Mapping of Short Biological Sequences in High Performance Computational Environments

La bioinformática es la aplicación de las ciencias computacionales a la gestión y análisis de datos biológicos. A partir de 2005, con la aparición de los secuenciadores de ADN de nueva generación surge lo que se conoce como Next Generation Sequencing o NGS. Un único experimento biológico puesto en marcha en una máquina de secuenciación NGS puede producir fácilmente cientos de gigabytes o incluso terabytes de datos. Dependiendo de la técnica elegida este proceso puede realizarse en unas pocas horas o días. La disponibilidad de recursos locales asequibles, tales como los procesadores multinúcleo o las nuevas tarjetas gráfi cas preparadas para el cálculo de propósito general GPGPU (General Purpose Graphic Processing Unit ), constituye una gran oportunidad para hacer frente a estos problemas. En la actualidad, un tema abordado con frecuencia es el alineamiento de secuencias de ADN. En bioinformática, el alineamiento permite comparar dos o más secuencias de ADN, ARN, o estructuras primarias proteicas, resaltando sus zonas de similitud. Dichas similitudes podrían indicar relaciones funcionales o evolutivas entre los genes o proteínas consultados. Además, la existencia de similitudes entre las secuencias de un individuo paciente y de otro individuo con una enfermedad genética detectada podría utilizarse de manera efectiva en el campo de la medicina diagnóstica. El problema en torno al que gira el desarrollo de la tesis doctoral consiste en la localización de fragmentos de secuencia cortos dentro del ADN. Esto se conoce bajo el sobrenombre de mapeo de secuencia o sequence mapping. Dicho mapeo debe permitir errores, pudiendo mapear secuencias incluso existiendo variabilidad genética o errores de lectura en el mapeo. Existen diversas técnicas para abordar el mapeo, pero desde la aparición de la NGS destaca la búsqueda por pre jos indexados y agrupados mediante la transformada de Burrows-Wheeler [28] (o BWT en lo sucesivo). Dicha transformada se empleó originalmente en técnicas de compresión de datos, como es el caso del algoritmo bzip2. Su utilización como herramienta para la indización y búsqueda posterior de información es más reciente [22]. La ventaja es que su complejidad computacional depende únicamente de la longitud de la secuencia a mapear. Por otra parte, una gran cantidad de técnicas de alineamiento se basan en algoritmos de programación dinámica, ya sea Smith-Watterman o modelos ocultos de Markov. Estos proporcionan mayor sensibilidad, permitiendo mayor cantidad de errores, pero su coste computacional es mayor y depende del tamaño de la secuencia multiplicado por el de la cadena de referencia. Muchas herramientas combinan una primera fase de búsqueda con la BWT de regiones candidatas al alineamiento y una segunda fase de alineamiento local en la que se mapean cadenas con Smith-Watterman o HMM. Cuando estamos mapeando permitiendo pocos errores, una segunda fase con un algoritmo de programación dinámica resulta demasiado costosa, por lo que una búsqueda inexacta basada en BWT puede resultar más e ficiente. La principal motivación de la tesis doctoral es la implementación de un algoritmo de búsqueda inexacta basado únicamente en la BWT, adaptándolo a las arquitecturas paralelas modernas, tanto en CPU como en GPGPU. El algoritmo constituirá un método nuevo de rami cación y poda adaptado a la información genómica. Durante el periodo de estancia se estudiarán los Modelos ocultos de Markov y se realizará una implementación sobre modelos de computación funcional GTA (Aggregate o Test o Generate), así como la paralelización en memoria compartida y distribuida de dicha plataforma de programación funcional.Salavert Torres, J. (2014). Inexact Mapping of Short Biological Sequences in High Performance Computational Environments [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/43721TESI

Análisis y propuesta de mejora de la administración electrónica de la Diputación de Valencia

[ES] El presente estudio consiste en la elaboración del Trabajo Fin de Grado que es necesario realizar para la obtención del título de Graduado en gestión y Administración Pública que se imparte en la facultad de Administración y Dirección de Empresas de la Universidad Politécnica de Valencia. Este TFG trata de analizar los servicios electrónicos que en la actualidad presta la Diputación Provincial de Valencia, de qué manera se gestionan y proponer mejoras organizativas, procedimentales y de sistemas de información para el buen funcionamiento de los mismos.[EN] The present study consists in developing the Final Project is required to obtain the Certificate in Public Administration and Management, taught in the Faculty of Business Administration at the Polytechnic University of Valencia. This TFG attempts to analyze the electronic services currently provided by the Provincial Council of Valencia, in what way are managed and propose organizational, procedural and information systems for the proper functioning of these improvements.[CA] El present estudi consistix en l’elaboració del Treball Final de Grau que és necessari realitzar per a l'obtenció del títol de Graduat en Gestió i Administració Pública que s’impartix en la facultad d’Administració i Direcció d’Empreses de la Universitat Politecnica de València. Aquest TFG tracta d’analitzar els servicis electrònics que en l’actualitat presta la Diputació Provincial de València, de quina manera es gestionen i proposar millores organitzatives, procedimentals i de sistemes d’informaciò per al bon funcionament dels mateixosSalavert Griñón, JR. (2014). Análisis y propuesta de mejora de la Administración Electrónica de la Diputación de Valencia. http://hdl.handle.net/10251/43417.Archivo delegad

Towards Inter-Subject Project-Based Learning in Programming-Related Courses at Computer Science Studies

[EN] Curriculum design of University Degrees in Spain is mainly based on scheduling atomic, self-contained semester subjects during a 4-year period. This scheduling is driven by one major constraint: to ensure that previous subject pre-requisites are met for each course. Thus, basic subjects without college-level pre-requisites are typically scheduled in the first year, first semester, while the rest are properly planned in a sequential manner, complying the aforementioned condition. This is, basically, the only proof of inter-subject coordination in such degrees, taking place at the design stage. During the academic period, however, there is no vertical nor horizontal inter-subject coordination, not even among closely-related subjects. In order to increase inter-subject coordination and to exploit its potential benefit for students, the projectbased learning (PBL) methodology shows on the scene. This approach organizes learning around student-driven projects aiming to solve real-life problems. This close applicability to the real world expedites intrinsic motivation of students, and consequently, their learning process tends to be deeper and more significant. Furthermore, PBL applied at the inter-subject level increases curriculum cohesion and makes students more engaged and compromised with its global objectives. In this paper we describe the design of PBL models involving two pairs of programming-related subjects from the Computer Engineering Degree at the Universitat Politècnica de València. The first one associates the ¿Programming¿ with the ¿Data Structures and Algorithms¿ subject, while the second one engages the ¿Introduction to Video-Games Programming¿ with the ¿Digital Image Synthesis¿ one. It is an ambitious pilot programme that will require a high coordination effort among participating professors and student teams.This article has been supported by the Vice-rectorate for Digital Resources and Documentation (Vicerrectorado de Recursos Digitales y Documentación) and Vice-Rectorate for Studies, Quality and Accreditation (Vicerrectorado de Estudios, Calidad y Acreditación) under the Call for Learning + Teaching (Convocatoria Aprendizaje + Docencia (A+D 2019)) and Project Code: 1678-A. The authors would like to acknowledge the support of the Institute of Educational Sciences (Instituto de Ciencias de la Educación) of Universitat Politècnica de València, the Evaluation and Monitoring Commission for Educational Innovation and Improvement Projects (Comisión de Evaluación y Seguimiento de Proyectos de Innovación y Mejora Educativa (CESPIME)) and Escuela Politécnica Superior de AlcoyLinares-Pellicer, J.; Orta-López, J.; Salavert-Torres, J.; Segura Flor, MJ.; Silvestre Cerdà, JA.; Sanchis, R. (2020). Towards Inter-Subject Project-Based Learning in Programming-Related Courses at Computer Science Studies. EDULEARN Proceedings (Internet). 3973-3978. https://doi.org/10.21125/edulearn.2020.1075S3973397

Consequences of using biodiesel on the injection and air-fuel mixing processes in diesel engines

(c) IMechE 2013A study of the injection process and spray behaviour was made for three different fuels. In particular, blends of rapeseed methyl ester and standard diesel fuel with 5% and 30% biodiesel were used for the current study, as well as pure rapeseed methyl ester. Hydraulic characterization of an eight-hole nozzle was carried out using these three fuels, in order to explore and analyse the influence of the fuel properties on the mass flow rate and the momentum flux at the nozzle exit. Additionally, spray visualization tests were performed in order to obtain information about the spray cone angle, which allows characterization of the air-fuel mixing process. Finally, a theoretical derivation was used to obtain further details of the microscopic characteristics of the spray and to compare the air-fuel mixing efficiencies for the different biodiesel blends.This work was partly supported by Vicerrectorado de Investigacion, Desarrollo e Innovacion of the Universitat Politecnica de Valencia in the framework of the Project Estudio del Flujo en Toberas de Inyeccion Diesel Mediante Tecnicas LES (project no. 2837) and by Ministerio de Ciencia e Innovacion in the framework of the Project Estudio Teorico-experimental sobre la Influencia del Tipo de Combustible en Los Procesos de Atomizacion y Evaporacion del Chorro Diesel (project no. TRA2011-26293).Salvador Rubio, FJ.; Ruiz Rosales, S.; Salavert Fernández, JM.; De La Morena Borja, J. (2013). Consequences of using biodiesel on the injection and air-fuel mixing processes in diesel engines. Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering. 227(8):1130-1141. https://doi.org/10.1177/0954407012463667S113011412278Altın, R., Çetinkaya, S., & Yücesu, H. S. (2001). The potential of using vegetable oil fuels as fuel for diesel engines. Energy Conversion and Management, 42(5), 529-538. doi:10.1016/s0196-8904(00)00080-7Rakopoulos, C. D., Antonopoulos, K. A., Rakopoulos, D. C., Hountalas, D. T., & Giakoumis, E. G. (2006). Comparative performance and emissions study of a direct injection Diesel engine using blends of Diesel fuel with vegetable oils or bio-diesels of various origins. Energy Conversion and Management, 47(18-19), 3272-3287. doi:10.1016/j.enconman.2006.01.006Agarwal, A. K. (2007). Biofuels (alcohols and biodiesel) applications as fuels for internal combustion engines. Progress in Energy and Combustion Science, 33(3), 233-271. doi:10.1016/j.pecs.2006.08.003Basha, S. A., Gopal, K. R., & Jebaraj, S. (2009). A review on biodiesel production, combustion, emissions and performance. Renewable and Sustainable Energy Reviews, 13(6-7), 1628-1634. doi:10.1016/j.rser.2008.09.031Luján, J. M., Bermúdez, V., Tormos, B., & Pla, B. (2009). Comparative analysis of a DI diesel engine fuelled with biodiesel blends during the European MVEG-A cycle: Performance and emissions (II). Biomass and Bioenergy, 33(6-7), 948-956. doi:10.1016/j.biombioe.2009.02.003Golovitchev, V. I., & Yang, J. (2009). Construction of combustion models for rapeseed methyl ester bio-diesel fuel for internal combustion engine applications. Biotechnology Advances, 27(5), 641-655. doi:10.1016/j.biotechadv.2009.04.024LAPUERTA, M., ARMAS, O., & RODRIGUEZFERNANDEZ, J. (2008). Effect of biodiesel fuels on diesel engine emissions. Progress in Energy and Combustion Science, 34(2), 198-223. doi:10.1016/j.pecs.2007.07.001Payri, F., Bermúdez, V., Payri, R., & Salvador, F. J. (2004). The influence of cavitation on the internal flow and the spray characteristics in diesel injection nozzles. Fuel, 83(4-5), 419-431. doi:10.1016/j.fuel.2003.09.010Jung, K., Khil, T., & Yoon, Y. (2006). Effects of Orifice Internal Flow on Breakup Characteristics of like-Doublet Injectors. Journal of Propulsion and Power, 22(3), 653-660. doi:10.2514/1.20362Park, S. H., Suh, H. K., & Lee, C. S. (2008). Effect of Cavitating Flow on the Flow and Fuel Atomization Characteristics of Biodiesel and Diesel Fuels. Energy & Fuels, 22(1), 605-613. doi:10.1021/ef7003305PAYRI, R., GARCIA, J., SALVADOR, F., & GIMENO, J. (2005). Using spray momentum flux measurements to understand the influence of diesel nozzle geometry on spray characteristics. Fuel, 84(5), 551-561. doi:10.1016/j.fuel.2004.10.009Pastor, J. V., Arrègle, J., García, J. M., & Zapata, L. D. (2007). Segmentation of diesel spray images with log-likelihood ratio test algorithm for non-Gaussian distributions. Applied Optics, 46(6), 888. doi:10.1364/ao.46.000888Desantes, J. M., Payri, R., Garcia, J. M., & Salvador, F. J. (2007). A contribution to the understanding of isothermal diesel spray dynamics. Fuel, 86(7-8), 1093-1101. doi:10.1016/j.fuel.2006.10.011Desantes, J. M., Salvador, F. J., López, J. J., & De la Morena, J. (2010). Study of mass and momentum transfer in diesel sprays based on X-ray mass distribution measurements and on a theoretical derivation. Experiments in Fluids, 50(2), 233-246. doi:10.1007/s00348-010-0919-8Salvador, F. J., Ruiz, S., Gimeno, J., & De la Morena, J. (2011). Estimation of a suitable Schmidt number range in diesel sprays at high injection pressure. International Journal of Thermal Sciences, 50(9), 1790-1798. doi:10.1016/j.ijthermalsci.2011.03.030Payri, R., Tormos, B., Salvador, F. J., & Araneo, L. (2008). Spray droplet velocity characterization for convergent nozzles with three different diameters. Fuel, 87(15-16), 3176-3182. doi:10.1016/j.fuel.2008.05.028Luján, J. M., Tormos, B., Salvador, F. J., & Gargar, K. (2009). Comparative analysis of a DI diesel engine fuelled with biodiesel blends during the European MVEG-A cycle: Preliminary study (I). Biomass and Bioenergy, 33(6-7), 941-947. doi:10.1016/j.biombioe.2009.02.004Salvador, F. J., Martínez-López, J., Romero, J.-V., & Roselló, M.-D. (2011). Influence of biofuels on the internal flow in diesel injector nozzles. Mathematical and Computer Modelling, 54(7-8), 1699-1705. doi:10.1016/j.mcm.2010.12.010Desantes, J. M., Payri, R., Salvador, F. J., & Gil, A. (2006). Development and validation of a theoretical model for diesel spray penetration. Fuel, 85(7-8), 910-917. doi:10.1016/j.fuel.2005.10.023Wang, X., Huang, Z., Kuti, O. A., Zhang, W., & Nishida, K. (2010). Experimental and analytical study on biodiesel and diesel spray characteristics under ultra-high injection pressure. International Journal of Heat and Fluid Flow, 31(4), 659-666. doi:10.1016/j.ijheatfluidflow.2010.03.006Pogorevc, P., Kegl, B., & Skerget, L. (2008). Diesel and Biodiesel Fuel Spray Simulations. Energy & Fuels, 22(2), 1266-1274. doi:10.1021/ef700544rGao, Y., Deng, J., Li, C., Dang, F., Liao, Z., Wu, Z., & Li, L. (2009). Experimental study of the spray characteristics of biodiesel based on inedible oil. Biotechnology Advances, 27(5), 616-624. doi:10.1016/j.biotechadv.2009.04.022Lee, C. S., Park, S. W., & Kwon, S. I. (2005). An Experimental Study on the Atomization and Combustion Characteristics of Biodiesel-Blended Fuels. Energy & Fuels, 19(5), 2201-2208. doi:10.1021/ef050026hKamrak, J., Kongsombut, B., Grehan, G., Saengkaew, S., Kim, K.-S., & Charinpanitkul, T. (2009). Mechanistic study on spraying of blended biodiesel using phase Doppler anemometry. Biomass and Bioenergy, 33(10), 1452-1457. doi:10.1016/j.biombioe.2009.06.011Payri, R., Salvador, F. J., Gimeno, J., & Zapata, L. D. (2008). Diesel nozzle geometry influence on spray liquid-phase fuel penetration in evaporative conditions. Fuel, 87(7), 1165-1176. doi:10.1016/j.fuel.2007.05.05

Biomarkers of fungal infection: Expert opinion on the current situation

The introduction of non-culture-based diagnostic techniques is revolutionizing the world of microbiological diagnosis and infection assessment. Fungi are no exception, and the introduction of biomarkers has opened up enormous expectations for better management of these entities. Biomarkers are diverse, their targets are also diverse and their evaluation has been done preferably in an individualized use and with deficient designs. Less is known about the value of the combined use of biomarkers and the impact of the negativity of two or more biomarkers on antifungal treatment decisions has been poorly studied. Given the paucity of prospective, randomized and definitive studies, we have convened experts from different fields, with an interest in invasive fungal infections, to answer some questions about the current relevant use of fungal biomarkers. This document summarizes the answers of these experts to the different questions

Dalbavancin in clinical practice in Spain: a 2 year retrospective study

Objectives Dalbavancin is approved for the treatment of acute bacterial skin and skin-structure infections (ABSSSIs) in adults. Its unique pharmacokinetic properties allow daily dosing to be avoided. The objective was to describe the sociodemographic and clinical characteristics of patients treated with dalbavancin in Spain, and to evaluate its effectiveness and safety in real-world settings. Patients and methods This non-interventional, retrospective, observational and multicentre study included patients who received at least one dose between 2018 and 2019 in seven Spanish hospitals. Results In total, 187 patients were included. The most common comorbidities were cardiovascular disease (27.4%) and diabetes mellitus (23.5%). Dalbavancin was used to treat osteoarticular infections (28.3%), ABSSSIs (22.5%), cardiovascular infections (20.9%) and catheter-related infections (18.2%). The most prevalent pathogens were Staphylococcus aureus (34.2%), CoNS (32.6%), and enterococci (12.8%). The main reason for use was early hospital discharge (65.8%). Most patients were treated with 1500 mg in a single dose (35.3%) and the median duration of treatment was 2 weeks. The treatment was clinically successful in 91.4% of cases. Six patients (3.2%) reported adverse events. Physicians agreed on the potential reduction of hospitalization days (85.3%). A subanalysis of patient characteristics and type of pathogen showed similar results in terms of efficacy and safety. Conclusions Dalbavancin seems to be effective and safe as second-line treatment in severe Gram-positive infections. It improves treatment adherence and allows outpatient management. Furthermore, the effectiveness and safety profile are maintained against diverse microorganisms in Gram-positive infections and regardless of the patients' comorbidities at baseline, or age

Bibliografía histórica sobre la ciencia y la técnica en España, 2004

Peer reviewedFecha 2014-09-15.--Fujitsu ScanSnap iX500.--Unidad técnica IHMC.--Archivo depósito IHMC.--Solo se permite el uso con fines educativos y de investigació

Exchanging Data for Breast Cancer Diagnosis on Heterogeneous Grid Platforms

This article describes the process of defining and implementing new components to exchange data between two real GRID-based platforms for breast cancer diagnosis. This highly collaborative work in development phase pretends to allow communication between middleware, namely TRENCADIS and DRI, in different virtual organizations. On the one hand, TRENCADIS is a Service-Oriented Architecture in which the usage of resources is represented with Grid services based on the Open Grid Service Architecture specification (OGSA).On the other hand, DRI is a software platform aimed at reducing the cost of hosting digital repositories of arbitrary nature on Grid infrastructures. TRENCADIS has been deployed in the Dr. Peset Hospital (Valencia, Spain) and DRI has been deployed in the S ao Jo ao Hospital (Porto, Portugal). The final objective of this work in progress is to share medical images and its associated metadata among geographically distributed research institutions, while maintaining confidentiality and privacy of data

Model-Driven Development of Aspect-Oriented Software Architectures

[EN] The Model-Driven Development (MDD) paradigm has become widely spread in the last few years due to being based on models instead of source code, and using automatic generation techniques to obtain the final software product. Until now, the most mature methodologies that have been proposed to develop software following MDD are mainly based on functional requirements by following the Object-Oriented Paradigm. Therefore, mature MDD methodologies are required for supporting the code generation from models that specify non-functional requirements. The Aspect-Oriented Software Development (AOSD) approach was created to provide explicit mechanisms for developing non-functional requirements through reusable elements called aspects. Aspect-Oriented Software Architectures (AOSA) emerged to deal with the design of both, functional requirements and non-functional requirements, which opened an important challenge in the software engineering field: the definition of a methodology for supporting the development of AOSAs following the MDD paradigm. This new methodology should allow the code generation from models which specify functional and non-functional requirements. This paper presents a mature approach, called PRISMA, which deals with this challenge. Therefore, this contribution takes a step forward in the area presenting in detail the PRISMA MDD process, which has been applied to generate the code of several real applications of the tele-operated robotics domain. PRISMA MDD approach provides complete support for the development of technology-independent AOSAs, which can be compiled from high-level, aspect-oriented architectural models into different technology platforms and languages following an MDD process. This contribution illustrates how to apply the PRISMA MDD approach through the modelling framework that has been developed to support it, and a case study of a tele-operated robot that has been completely developed using this approach. Finally, the results obtained from the application of PRISMA MDD process to develop applications of the tele-operation domain are analyzed in terms of code generation.The work reported here has been partially sponsored by the Spanish MEC projects (DSDM TIN2008-00889-E and MULTIPLE TIN2009-13838), and MICINN (INNOSEP TIN2009-13849)Pérez Benedí, J.; Ramos Salavert, I.; Carsí Cubel, JÁ.; Costa Soria, C. (2013). Model-Driven Development of Aspect-Oriented Software Architectures. Journal of Universal Computer Science. 19(10):1433-1473. https://doi.org/10.3217/jucs-019-10-143314331473191

Bibliografía histórica sobre la ciencia y la técnica en España. 1989

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