Visualización y simulación de las interacciones de la red de proteínas del Potyvirus del tabaco

[ES] En el marco de un trabajo en colaboración con el Grupo de Virología Evolutiva del IBMCP, y la Unidad de Biología Computacional del Centro Príncipe Felipe (CIPF), se está trabajando en la dilucidación de la red dinámica de interacciones entre las 11 proteínas que constituyen los potyvirus de la planta del tabaco. Este tipo de virus sirve de modelo para el estudio de otros virus semejantes, como el de la hepatitis C. El análisis posterior de la dinámica de la red (análisis de sensitividad, conectividad, dinámica reproductiva, etc.) se espera sirva para una comprensión de la capacidad del potyvirus para escapar a los mecanismos de protección puestos en marcha por la planta infectada y, del mismo modo, para detectar las interacciones más sensibles a efectos de combatir la reproducción del virus. El trabajo mencionado corresponde a un proyecto a medio-largo plazo con muchas etapas intermedias. En el trabajo aquí propuesto se tratarán aspectos parciales, fundamentalmente relacionados con temas de estructuración y visualización de información en redes de interacciones. Se tratará sobre todo de trabajos de extensión y aplicación del software Cell Browser desarrollado en el CIPF. En el trabajo se plantean varios subobjetivos: - Extensión de Cell Browser para poder implementar la red de interacciones de las proteínas del potyvirus. - Implementación de medidas de la red. Existen en la literatura toda una serie de métricas que permiten el análisis topológico de redes. Las medidas para redes no dirigidas son aplicables en la red bajo estudio. Desde el punto de vista didáctico, en esta parte se tratará sobre el análisis topológico de redes.[EN] As part of a collaboration with the Group of Evolutionary Virology IBMCP, and Computational Biology Unit Prince Felipe Center (CIPF), it is working on the elucidation of the dynamic network of interactions among 11 proteins that constitute the Plant potyvirus snuff. This type of virus is a model for the study of other viruses such as hepatitis C. Subsequent analysis of network dynamics (sensitivity analysis, connectivity, reproductive dynamics, etc.) is expected to serve for understanding potyvirus's ability to escape protection mechanisms implemented by the infected plant and, likewise, to detect the most sensitive in order to combat the virus from reproducing interactions. The work mentioned corresponds to a project in the medium to long term with many intermediate stages. At work here proposed partial aspects will be discussed mainly issues related to structuring and displaying information in networks of interactions. It will be especially extension work and implementation of the Cell Browser software developed in the CIPF. There sub-objectives are: - Cell Browser Extension to implement the network of interactions between proteins potyvirus. - Implementation of measures in the network. In the literature, exists a series of metrics to the topological analysis of networks. The measures for undirected are applicable to the network under study. From the educational point of view, this part will be discussed on the topological analysis of networks.Salavert Torres, F. (2015). Visualización y simulación de las interacciones de la red de proteínas del Potyvirus del tabaco. http://hdl.handle.net/10251/54165TFG

Implementación de un regulador PID en un dsPIC33F

Salavert Torres, F. (2010). Implementación de un regulador PID en un dsPIC33F. http://hdl.handle.net/10251/10300.Archivo delegad

An efficient synthesis of new fluorinated uracil derivatives

A series of potentially biologically active fluorinated uracil derivatives has been prepared in three steps from oxazolines and fluorinated nitriles with good chemical yields.Fustero Lardies, Santos, [email protected] ; Sanz Cervera, Juan Francisco, [email protected] ; Asensio Martinez, Amparo, [email protected]

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

Ten Issues for Updating in Community-Acquired Pneumonia: An Expert Review

Aetiology; Community acquired pneumonia; Radiologic findingsEtiologia; Pneumònia adquirida a la comunitat; Troballes radiològiquesEtiología; Neumonía adquirida en la comunidad; Hallazgos radiológicosCommunity-acquired pneumonia represents the third-highest cause of mortality in industrialized countries and the first due to infection. Although guidelines for the approach to this infection model are widely implemented in international health schemes, information continually emerges that generates controversy or requires updating its management. This paper reviews the most important issues in the approach to this process, such as an aetiologic update using new molecular platforms or imaging techniques, including the diagnostic stewardship in different clinical settings. It also reviews both the Intensive Care Unit admission criteria and those of clinical stability to discharge. An update in antibiotic, in oxygen, or steroidal therapy is presented. It also analyzes the management out-of-hospital in CAP requiring hospitalization, the main factors for readmission, and an approach to therapeutic failure or rescue. Finally, the main strategies for prevention and vaccination in both immunocompetent and immunocompromised hosts are reviewed

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

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

The discovery of actionable targets is crucial for targeted therapies and is also a constituent part of the drug discovery process. The success of an intervention over a target depends critically on its contribution, within the complex network of gene interactions, to the cellular processes responsible for disease progression or therapeutic response. Here we present PathAct, a web server that predicts the effect that interventions over genes (inhibitions or activations that simulate knock-outs, drug treatments or over-expressions) can have over signal transmission within signaling pathways and, ultimately, over the cell functionalities triggered by them. PathAct implements an advanced graphical interface that provides a unique interactive working environment in which the suitability of potentially actionable genes, that could eventually become drug targets for personalized or individualized therapies, can be easily tested. The PathAct tool can be found at: http://pathact.babelomics.org.Spanish Ministry of Economy and Competitiveness [BIO2014-57291-R]; ‘Plataforma de Recursos Biomoleculares y Bioinformáticos’ PT 13/0001/0030 from the ISCIII; co-funded with European Regional Development Funds (ERDF); Generalitat Valenciana (GVA-FEDER) [PROMETEOII/2014/025]; Fundació la Marató TV3 [20133134]; EU FP7-People ITN Marie Curie Project [ref 316861]; EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE [ref 676559]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2014-57291-R]

Bibliografía histórica sobre la ciencia y la técnica en España, 2001-2002

Repertori de bibliografia històrica sobre la ciència i la tècnica a Espanya editada en 2001-2002. //.Repertorio de bibliografía histórica sobre la ciencia y la técnica en España editada en 2001-200

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.The Spanish Ministry of Science and Innovation (MICINN) [BIO2011-27069]; the Conselleria de Educacio of the Valencian Community [PROMETEO/2010/001]; National Institute of Bioinformatics (www.inab.org); CIBER de Enfermedades Raras (CIBERER), ISCIII and MICINN; Red Tematica de Investigacion Cooperativa en Cancer (RTICC) [RD06/0020/1019] ISCIII, MICINN and INNPACTO [IPT-010000-2010-43], MICINN. Funding for open access charge: MICINN [BIO2011-27069].Bleda, M.; Tarraga, J.; De María, A.; Salavert, F.; García-Alonso, L.; Celma Giménez, M.; Martín Mayordomo, A.... (2012). CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Research. 40(1):609-614. https://doi.org/10.1093/nar/gks575S609614401Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., … Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. doi:10.1038/nbt1346Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., … Fitzgerald, S. (2011). Ensembl 2012. Nucleic Acids Research, 40(D1), D84-D90. doi:10.1093/nar/gkr991(2011). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Research, 40(D1), D71-D75. doi:10.1093/nar/gkr981Kozomara, A., & Griffiths-Jones, S. (2010). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research, 39(Database), D152-D157. doi:10.1093/nar/gkq1027Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., & Li, T. (2009). miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Research, 37(Database), D105-D110. doi:10.1093/nar/gkn851Hsu, S.-D., Lin, F.-M., Wu, W.-Y., Liang, C., Huang, W.-C., Chan, W.-L., … Huang, H.-D. (2010). miRTarBase: a database curates experimentally validated microRNA–target interactions. Nucleic Acids Research, 39(suppl_1), D163-D169. doi:10.1093/nar/gkq1107Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2008). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), 92-105. doi:10.1101/gr.082701.108Betel, D., Wilson, M., Gabow, A., Marks, D. S., & Sander, C. (2007). The microRNA.org resource: targets and expression. Nucleic Acids Research, 36(Database), D149-D153. doi:10.1093/nar/gkm995Dreszer, T. R., Karolchik, D., Zweig, A. S., Hinrichs, A. S., Raney, B. J., Kuhn, R. M., … James Kent, W. (2011). The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research, 40(D1), D918-D923. doi:10.1093/nar/gkr1055Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., … Yong, S.-Y. (2011). InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research, 40(D1), D306-D312. doi:10.1093/nar/gkr948Sherry, S. T. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308-311. doi:10.1093/nar/29.1.308(2010). Integrating common and rare genetic variation in diverse human populations. Nature, 467(7311), 52-58. doi:10.1038/nature09298(2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073. doi:10.1038/nature09534Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009). Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences, 106(23), 9362-9367. doi:10.1073/pnas.0903103106Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S. T., … Cooper, D. N. (2003). Human Gene Mutation Database (HGMD®): 2003 update. Human Mutation, 21(6), 577-581. doi:10.1002/humu.10212Johnson, A. D., & O’Donnell, C. J. (2009). An Open Access Database of Genome-wide Association Results. BMC Medical Genetics, 10(1). doi:10.1186/1471-2350-10-6Forbes, S. A., Bindal, N., Bamford, S., Cole, C., Kok, C. Y., Beare, D., … Futreal, P. A. (2010). COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Research, 39(Database), D945-D950. doi:10.1093/nar/gkq929Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., … Hermjakob, H. (2011). The IntAct molecular interaction database in 2012. Nucleic Acids Research, 40(D1), D841-D846. doi:10.1093/nar/gkr1088Croft, D., O’Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., … Stein, L. (2010). Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research, 39(Database), D691-D697. doi:10.1093/nar/gkq1018Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., … Luciano, J. (2010). The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28(9), 935-942. doi:10.1038/nbt.1666Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., … Goble, C. A. (2010). BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research, 38(Web Server), W689-W694. doi:10.1093/nar/gkq394Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R., & Stein, L. (2001). BMC Bioinformatics, 2(1), 7. doi:10.1186/1471-2105-2-

Ten Issues for Updating in Community-Acquired Pneumonia: An Expert Review

Community-acquired pneumonia represents the third-highest cause of mortality in industrialized countries and the first due to infection. Although guidelines for the approach to this infection model are widely implemented in international health schemes, information continually emerges that generates controversy or requires updating its management. This paper reviews the most important issues in the approach to this process, such as an aetiologic update using new molecular platforms or imaging techniques, including the diagnostic stewardship in different clinical settings. It also reviews both the Intensive Care Unit admission criteria and those of clinical stability to discharge. An update in antibiotic, in oxygen, or steroidal therapy is presented. It also analyzes the management out-of-hospital in CAP requiring hospitalization, the main factors for readmission, and an approach to therapeutic failure or rescue. Finally, the main strategies for prevention and vaccination in both immunocompetent and immunocompromised hosts are reviewed