Edward E. O''Brien contributions to reactive-flow turbulence

Professor Edward Ephraim O''Brien (“Ted”) has made lasting contributions to the theory and modeling of scalar mixing and reaction in turbulent flows. With a doctoral dissertation at The Johns Hopkins University in 1960, entitled “On the Statistical Behavior of a Dilute Reactant in Isotropic Turbulence, ” supervised by the legend Stanley Corrsin, and in the company of notable pioneer of turbulence, John Leask Lumley, Ted''s academic training propelled him through a prolific career. In the opening article of this Special Issue, we provide a review of some of Ted''s contributions. First, a summary is presented of his work on the examination of the failure of the cumulant discard approximation for the scalar mixing. This is followed by a highlight of his impacts on other spectral theories of turbulence including Kraichnan''s direct interaction approximation. His contributions to more modern theoretical/computational description of reactive turbulence are discussed next, including the transported probability density function (pdf) formulation, scalar-gradient pdf transport equation, scalar interfaces, and the filtered density function. Finally, some of his research on Direct Numerical Simulation of compressible turbulence is reviewed. © 2021 Author(s)

Liquid compressibility effects during the collapse of a single cavitating bubble

The effect of liquid compressibility on the dynamics of a single, spherical cavitating bubble is studied. While it is known that compressibility damps the amplitude of bubble rebounds, the extent to which this effect is accurately captured by weakly compressible versions of the Rayleigh–Plesset equation is unclear. To clarify this issue, partial differential equations governing conservation of mass, momentum, and energy are numerically solved both inside the bubble and in the surrounding compressible liquid. Radiated pressure waves originating at the unsteady bubble interface are directly captured. Results obtained with Rayleigh–Plesset type equations accounting for compressibility effects, proposed by Keller and Miksis [J. Acoust. Soc. Am. 68, 628–633 (1980)], Gilmore, and Tomita and Shima [Bull. JSME 20, 1453–1460 (1977)], are compared with those resulting from the full model. For strong collapses, the solution of the latter reveals that an important part of the energy concentrated during the collapse is used to generate an outgoing pressure wave. For the examples considered in this research, peak pressures are larger than those predicted by Rayleigh–Plesset type equations, whereas the amplitudes of the rebounds are smaller

Local entrainment velocity in a premixed turbulent annular jet flame

The local entrainment velocity of the enstrophy interfaces of a methane-air turbulent premixed turbulent annular jet flame stabilized on a bluff-body burner has been investigated using a high-fidelity flame-resolved three-dimensional simulation. The enstrophy (inner and outer) and the scalar interfaces have been defined and characterized by their propagation speeds, VE and Sd , relative to the fluid flow. Mean values ( and ) conditioned on the reaction progress variable c have been obtained. A thin layer (near the enstrophy interfaces) has been used to compute mean values (, , and its different contributions) conditional upon enstrophy E. At the inner interface, results indicate that . Sd |. E> > 0 (entrainment of fresh reactants into the flame front and hot products), while < 0 and < 0 (entrainment of hot products into the reacting jet across the inner enstrophy interface). The outer enstrophy interface displays > 0 (ambient gases are predominantly entrained into the jet of reactants), which implies a lean mixture in its neighborhood. These preliminary results aim at understanding the physical mechanisms of flame anchoring, in terms of entrainments of either hot products or fresh reactants into the diffusive-reactive region. Local geometries of the inner and outer interfaces have also been examined, through the computation of joint probability density functions of the mean curvature km and Gauss curvature kg of the iso-enstrophy surfaces, and through |. km, kg at the inner and outer interfaces. This information has subsequently been used to discuss the physics of how the turbulent entrainment process affects premixed flames

Water disinfection by hydrodynamic cavitation in a rotor-stator device

The efficiency of a rotor-stator device for water disinfection based on hydrodynamic cavitation is investigated. Water is infected with E. coli and E. faecalis with initial concentrations in the range 5 × 102–1.2 × 106 CFU/ml. Various geometries of the cavitation channel between rotor and stator are tested, achieving bacterial annihilation in less than 10 min of treatment times. Microorganism permanent elimination is verified via micro-seeding to discard viable non-culturable bacteria; micro-seeding was done for those samples displaying no CFU growth via normalized cultures on a Petri dish. TEM photographs are analyzed and the extent of bacterial damages is tentatively correlated with the various cavitation mechanisms. Rotor-stator cavitation assemblies used in the current research are between one and two orders of magnitude more energy efficient than those tested by other investigators. Acoustic pressure spectra are measured to assess the implosion intensity. Parametric analyses are conducted changing the rotor diameter (110–155 mm), the cavitation channel contraction ratio, Amax/Amin(4.56–5.0), and the number of contractions (Nr:58–80 rotor vanes; Ns:8–16 stator vanes)

HCAD, closing the gap between breakpoints and genes

Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information system that mines the scientific literature and generates textual and comprehensive information on all human breakpoints. We show that the statistical analysis of this textual information and its combination with genomic data can identify genes directly involved in DNA rearrangements. The Human Chromosome Aberration Database (HCAD) is publicly accessible at http://www.pdg.cnb.uam.es/UniPub/HCAD/

Antemortem versus postmortem methods for detection of betanodavirus in Senegalese sole (Solea senegalensis)

The suitability of nested reverse transcription polymerase chain reaction (nRT-PCR) to detect betanodavirus in blood samples from naturally infected Senegalese sole (Solea senegalensis) was evaluated in comparison with other diagnostic methods. Results indicated that histologic examination of brain lesions could be regarded as the most consistent indicator of nodavirus infection in this species. The nRT-PCR showed low to moderate levels of detection; the best values were obtained in brain samples followed by blood samples. Inoculation of SSN-1 and SAF-1 cells with fish samples did not cause cytopathic effect, although virus was detected by reverse transcription polymerase chain reaction in approximately 25% of the SSN-1 inoculated wells. The efficiency of detection of the viral genome was dramatically increased by the use of nRTPCR, reaching 90.6% of positives in brain samples and 84.4% in blood samples. The sensitivity and the negative predictive value of nRT-PCR in blood samples were slightly lower than those obtained using brain samples. Nevertheless, it is suggested that the advantage of being able to perform diagnosis on live fish adequately counterbalances the slightly lower sensitivity of nRT-PCR on blood samples. This technique is proposed as a useful tool, not only for the selection of nodavirus-free breeders but also to check the fish status during ongrowing

Pinus halepensis Mill. resin exploitation and pitch kilns on Ibiza (Balearic Islands, Spain)

[ES] Por sus características particulares, el aprovechamiento de resina en la isla de Ibiza se ha realizado hasta hace unas décadas siguiendo procedimientos arcaicos, basados en el tratamiento del árbol para la producción de madera enteada, la posterior extracción de esta madera y su procesado mediante destilación por combustión en hornos primitivos. Se trata de actividades ya abandonadas a lo largo del siglo XIX en la península ibérica, en parte desconocidas y sin apenas información publicada, como es el caso del tratamiento para la producción y aprovechamiento de la madera enteada. El objetivo es aportar nuevos conocimientos y contribuir a la descripción del proceso tradicional del aprovechamiento de productos resinosos de Pinus halepensis Mill. en la forma realizada en la isla de Ibiza, incluida la preparación del árbol para la producción de madera enteada, su extracción y el posterior procesado con técnicas rudimentarias de destilación de la madera en hornos de alquitrán. A partir de la recogida sobre el terreno de información oral, correspondiente a personas que han realizado la actividad o han tenido un contacto directo con antiguos trabajadores del sector, así como del reconocimiento de materiales e infraestructuras empleados, se aportan nuevos datos de los procedimientos empleados, así como de las características de los árboles y hornos utilizados. Se describe el tratamiento, el aprovechamiento de la madera enteada y el procesado de los productos resinosos hasta su venta tras la primera transformación. Se amplían las localizaciones de hornos existentes con dos nuevos hornos. Se discuten los posibles motivos del mantenimiento de esta actividad hasta hace pocas décadas.[EN] Due to Ibiza¿s singular characteristics, the exploitation of resin had been maintained until some decades ago in an archaic way, based on the treatment of the tree as a producer of fatwood, which was extracted and processed through slow, controlled combustion in primitive pitch kilns. In contrast, these activities were abandoned during the XIX century in the iberian peninsula, becoming partly unknown and little represented in the literature. The objective of this article is to contribute to the understanding of this ancient industry both with new information and knowledge and explaining the process required in traditional Pinus halepensis Mill. pitch fabrication. Tar production on Ibiza, including the tree preparation, fatwood extraction and its combustion as well as rudimentary distillation process in tar ovens has been studied by interviewing people who have worked in this sector or people who have been directly involved with former workers. Materials and infrastructures used have been examined and provide new data about the trees¿ and ovens¿ characteristics, as well as about the techniques traditionally used. The treatment of the tree is described, and so it is the extraction and uses of pine tar. Finally, two previously non-cited ovens are identified and located. The possible reasons for the late disappearance of these practices are also discussed.Ribas, VA.; Dopazo, C. (2020). El aprovechamiento de madera teosa de Pinus halepensis Mill. y los hornos de alquitrán en Ibiza (Islas Baleares). Cuadernos de la Sociedad Española de Ciencias Forestales (Online). 46(1):139-160. https://doi.org/10.31167/csecfv0i46.19885S139160461Boned, A., 2018. Comunicación personal.Boned, A., 2019. Comunicación personal.Bonet, A., 2018. Comunicación personal.Cardona, A., 2019. Comunicación personal.Consell d'Eivissa, 2019. Enciclopèdia d'Eivissa i Formentera. http://www.eeif.es/. Consulta: 15 de octubre de 2019.Fàbrega, A., 2006. La pega vegetal. Producció i pluriactivitat pagesa. Estudis d'Historia Agraria 19; 69-104.Gil, L., Valdés, C.M., Díaz-Fernández, P., 2002. La transformación histórica del paisaje forestal en las islas Baleares. Tercer Inventario Forestal Nacional 1997-2007. Ministerio de Medio Ambiente.Guerau, C., 1973. Los hornos de alquitrán, una explotación poco conocida de nuestros bosques. Revista Eivissa 3, 23-28.Iturralde J., Elorrieta O., 1914. Estudio sobre la resinación de los montes españoles en sus aspectos botánicos, forestal, industrial y económico. Instituto de Ingenieros Civiles. Madrid.Junta Intersindical de Resinas, 1950. Memoria del Plan Nacional de Resinas. Madrid.Marí, V., 2018. Comunicación personal.Marí, V., 2019. Comunicación personal.Michavila, A., 2010. Alquitraners dels nostres montes. Lo Senienc: memoria, natura y llengua 7, 11-16.Orduna, P., 2014. Aproximación etnohistórica al trabajo de la pez en las Bárdenas Reales (Navarra). Revista de Dialectología y Tradiciones Populares LXIX (2), 413-433.Prados, B. ca 198-]. Las pegueras.Real Academia Española, 2019. Diccionario de la lengua española, 23.ª ed., [versión 23.3 en línea]. https://dle.rae.es. Consulta: 20 de junio de 2020.Ribas, M., 2018. Comunicación personal.Ribas, V.A., 2019. Proyecto piloto de establecimiento de parcela de resinación de Pinus halepensis con objetivo múltiple en Sant Josep de Sa Talaia, Eivissa (Illes Balears). Trabajo Final de Grado. Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural. Universitat Politècnica de València. Valencia.S.E.C.F., sin fecha. Glosario Técnico Forestal de la Sociedad Española de Ciencias Forestales. http://secforestales.org/diccionario_forestal_secf. Consulta: 20 de junio de 2020.Tur, A., 2018. Comunicación personal.Vilà, J., 1953. Ibiza y Formentera, islas de la sal. Estudios Geográficos Instituto Juan Sebastián Elcano del CSIC XIV, 363-408

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape

BIO2014-57291-R and SAF2017-88908-R from the Spanish Ministry of Economy and Competitivenessgrant PI15/00854 from the FIS“Plataforma de Recursos Biomoleculares y Bioinformáticos” PT17/0009/0006 from the ISCIII, cofunded with European Regional Development FundsFP7-PEOPLE-2012-ITN MLPM2012EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERAT