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)

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

EFFICIENCY ANALYSIS OF A BOILER FOR SUSPENSION BURNING OF SUGAR CAN E BAGASSE

ABSTRACT The present paper describes the results of the retrofittin g of a bagasse-fired boiler (RETO CV 2518) in the sugar mil i "Amancio Rodriguez", located in Las Tunas, Cuba . Th e boiler was modified in arder to implement a suspensio n burning configuratio n Among other modifications, the distribution of combustio n air along the furnace was redesigned in arder to obtain a large-scale swirling movement pattern aboye the grate . As a result the new aerodynamic organization of the fuel-ai r mixture within the furnace was significantly improved . The combustion efficiency of the boiler before and after th e retrofitting is analyzed in this paper . The results of the analysis show that the gross efficiency calculated for th e modified boiler increased in 2 % . This difference is du e mainly to the decrease of the heat losses by mechanica l unburnt from about 4 % before the retrofitting to 1 .95 % with the new configuration

Joint PDF modelling of turbulent flow and dispersion in an urban street canyon

The joint probability density function (PDF) of turbulent velocity and concentration of a passive scalar in an urban street canyon is computed using a newly developed particle-in-cell Monte Carlo method. Compared to moment closures, the PDF methodology provides the full one-point one-time PDF of the underlying fields containing all higher moments and correlations. The small-scale mixing of the scalar released from a concentrated source at the street level is modelled by the interaction by exchange with the conditional mean (IECM) model, with a micro-mixing time scale designed for geometrically complex settings. The boundary layer along no-slip walls (building sides and tops) is fully resolved using an elliptic relaxation technique, which captures the high anisotropy and inhomogeneity of the Reynolds stress tensor in these regions. A less computationally intensive technique based on wall functions to represent boundary layers and its effect on the solution are also explored. The calculated statistics are compared to experimental data and large-eddy simulation. The present work can be considered as the first example of computation of the full joint PDF of velocity and a transported passive scalar in an urban setting. The methodology proves successful in providing high level statistical information on the turbulence and pollutant concentration fields in complex urban scenarios.Comment: Accepted in Boundary-Layer Meteorology, Feb. 19, 200

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.e

A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression

Background Recent observations point towards the existence of a large number of neighborhoods composed of functionally-related gene modules that lie together in the genome. This local component in the distribution of the functionality across chromosomes is probably affecting the own chromosomal architecture by limiting the possibilities in which genes can be arranged and distributed across the genome. As a direct consequence of this fact it is therefore presumable that diseases such as cancer, harboring DNA copy number alterations (CNAs), will have a symptomatology strongly dependent on modules of functionally-related genes rather than on a unique "important" gene. Methods We carried out a systematic analysis of more than 140,000 observations of CNAs in cancers and searched by enrichments in gene functional modules associated to high frequencies of loss or gains. Results The analysis of CNAs in cancers clearly demonstrates the existence of a significant pattern of loss of gene modules functionally related to cancer initiation and progression along with the amplification of modules of genes related to unspecific defense against xenobiotics (probably chemotherapeutical agents). With the extension of this analysis to an Array-CGH dataset (glioblastomas) from The Cancer Genome Atlas we demonstrate the validity of this approach to investigate the functional impact of CNAs. Conclusions The presented results indicate promising clinical and therapeutic implications. Our findings also directly point out to the necessity of adopting a function-centric, rather a gene-centric, view in the understanding of phenotypes or diseases harboring CNAs.Spanish Ministry of Science and Innovation (grant BIO2008-04212)Spanish Ministry of Science and Innovation (grant FIS PI 08/0440)GVA-FEDER (PROMETEO/2010/001)Red Temática de Investigación Cooperativa en Cáncer (RTICC) (grant RD06/0020/1019)Instituto de Salud Carlos III (ISCIII)Spanish Ministry of Science and InnovationSpanish Ministry of Health (FI06/00027

Definition of a list of fish diseases to aid health management in Spain

Trabajo presentado en la 14th EAFP International Conference (European Association of Fish Pathologists), celebrada en Praga (República Checa), del 14 al 19 de septiembre de 2009An expert working group used a risk ranking technique to compile a list of fish disease hazards (pathogens) of relevance to Spanish aquaculture. It was possible to divide the list into three groups: I-high national risk; II-regional risk; III-low risk. The three groups were as follows: Group I (high risk) Aphanomyces invadans (EUS)**, spring viraemia of carp virus (SVCV), koi herpes virus (KHV)¿ and infectious haematopoietic necrosis virus (IHNV)¿ Group II (regional risk) Enteromyxum spp. (leei and scophthalmi), Aquabirnaviridae (incl. IPNV), viral encephalopathy and retinopathy virus (VERV), Streptococcus iniae, Philasterides dicentrarchi and Aeromonas salmonicida (in the marine environment). Group III (low risk) Sparicotyle chrysophrii/Microcotylidae, Flavobacterium maritimus, Photobacterium piscicida, Togaviridae, Sphaerospora testicularis, Edwardsiella tarda, Birnavirus (no-EVE), Lactococcus garviae, viral haemorrhagic septicaemia virus (VHSV)¿, Tenacibaculum maritimum, epizootic haematopoietic necrosis virus (EHNV)**, Renibacterium salmoninarum (BKD) and Gyrodactylus salaris. The exercise formed part of a project concerning aquaculture health management (Jacumar-GESAC¿) in Spain and is being used to help define sampling plans for disease monitoring using epidemiological and risk-based criteria. **The diseases caused by these pathogens are notifiable and exotic according to Directive 2006/88/EC ¿The diseases caused by these pathogens are notifiable and non-exotic according to Directive 2006/88/EC ¿Plan Nacional de Cultivos Marinos; Gestión sanitaria de la acuicultura: Adaptación a la nueva normativa (GESAC) ¿ financed by the Junta Nacional Asesora de Cultivos Marinos (Jacumar

Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation.

Congenital disorders of glycosylation (CDG) are a heterogeneous and rapidly growing group of diseases caused by abnormal glycosylation of proteins and/or lipids. Mutations in genes involved in the homeostasis of the endoplasmic reticulum (ER), the Golgi apparatus (GA), and the vesicular trafficking from the ER to the ER-Golgi intermediate compartment (ERGIC) have been found to be associated with CDG. Here, we report a patient with defects in both N- and O-glycosylation combined with a delayed vesicular transport in the GA due to mutations in TRAPPC11, a subunit of the TRAPPIII complex. TRAPPIII is implicated in the anterograde transport from the ER to the ERGIC as well as in the vesicle export from the GA. This report expands the spectrum of genetic alterations associated with CDG, providing new insights for the diagnosis and the understanding of the physiopathological mechanisms underlying glycosylation disorders

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single gene classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single gene classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single gene classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single gene sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single gene classifiers for predicting outcome in breast cancer