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

Safety and effectiveness of a new electrical detachable microcoil for embolization of hemorrhoidal disease, November 2020–December 2021: results of a prospective study

Purpose: The purpose of this study was to prospectively evaluate the efficacy and safety of a new, bare platinum, detachable microcoil as a metallic embolization agent in the treatment of hemorrhoidal disease. Material and Methods: This prospective single-center study evaluated a new, bare platinum, electrical, detachable microcoil (Prestige plus coil (Balt Montmorency France)) for use in vascular embolization in patients with hemorrhoidal disease. Between January 2020 and January 2021, 24 embolization procedures were performed in 21 patients (12 males, 9 females; mean age 44.3 ± 7.3). The inclusion criteria were: (a) participants with grade I, II and III hemorrhoidal disease on the Goligher classification; (b) patients older than 18 years of age with a score of greater than 4 on the French bleeding score (FBS) scale; (c) patients with scores greater than 2 on the scale of discomfort proposed by Tradi and Farfallah. (d) patients who underwent treatment that included the use of the new novel coil (Prestige plus coil (Balt)) as an embolic material. The exclusion criteria were participants who failed to provide informed consent and participants diagnosed with rectal bleeding due to other causes (cancer, fissures or others). Participants with severe renal insufficiency, non-correctable coagulation abnormalities and adverse reactions to the contrast medium not correctable with medication were also excluded. The symptoms, technical aspects, the transarterial approach, clinical and technical success complications and short-term outcomes were assessed. Results: Technical success was obtained in 100% of the cases. Seventeen (80.9%) patients experienced improvements in their hemorrhoidal disease. The VAS and QL scores improved by 4 and 1.5 points (81.2% and 87.5%), respectively, after embolization (pV: 0001). Three (14.2%) patients underwent a second embolization due to rebleeding. One patient (4.7%) underwent surgery. No major complications were observed. Three patients had minor complications. The assessment of subjective post-treatment symptoms and QL surveys showed significant differences from the baseline survey. Likewise, the measurement of the degree of satisfaction using a telephone survey at 12 months revealed a high degree of patient satisfaction over 10 points (mean 8.3 ± 1.1). Conclusions: The present study demonstrates that the use of the new, platinum, detachable, electrical microcoil is safe and well-tolerated in the treatment of hemorrhoidal disease. Key points: Catheter-directed hemorrhoidal dearterialization (CDHD) is the procedure of embolization with embolic agents for the treatment of internal hemorrhoids. CDHD is a simple and safe procedure that is accepted by patients and preserves the anal sphincter; it presents few complications when metal devices or microspheres are used as embolic agents. As the recommended embolization agent in treatments, the Prestige electrical, detachable coil is a safe, easy-to-use and effective arterial embolic device

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs. We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting proteins. In order to make data available for understudied organisms, PTMcode v2 (http://ptmcode.embl.de) includes a new strategy to propagate PTMs from validated modified sites through orthologous proteins. The second release of PTMcode covers 19 eukaryotic species from which we collected more than 300 000 experimentally verified PTMs (>1 300 000 propagated) of 69 types extracting the post-translational regulation of >100 000 proteins and >100 000 interactions. In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs

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

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

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

Motivation: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways

Clustering of gene expression data: performance and similarity analysis

BACKGROUND: DNA Microarray technology is an innovative methodology in experimental molecular biology, which has produced huge amounts of valuable data in the profile of gene expression. Many clustering algorithms have been proposed to analyze gene expression data, but little guidance is available to help choose among them. The evaluation of feasible and applicable clustering algorithms is becoming an important issue in today's bioinformatics research. RESULTS: In this paper we first experimentally study three major clustering algorithms: Hierarchical Clustering (HC), Self-Organizing Map (SOM), and Self Organizing Tree Algorithm (SOTA) using Yeast Saccharomyces cerevisiae gene expression data, and compare their performance. We then introduce Cluster Diff, a new data mining tool, to conduct the similarity analysis of clusters generated by different algorithms. The performance study shows that SOTA is more efficient than SOM while HC is the least efficient. The results of similarity analysis show that when given a target cluster, the Cluster Diff can efficiently determine the closest match from a set of clusters. Therefore, it is an effective approach for evaluating different clustering algorithms. CONCLUSION: HC methods allow a visual, convenient representation of genes. However, they are neither robust nor efficient. The SOM is more robust against noise. A disadvantage of SOM is that the number of clusters has to be fixed beforehand. The SOTA combines the advantages of both hierarchical and SOM clustering. It allows a visual representation of the clusters and their structure and is not sensitive to noises. The SOTA is also more flexible than the other two clustering methods. By using our data mining tool, Cluster Diff, it is possible to analyze the similarity of clusters generated by different algorithms and thereby enable comparisons of different clustering methods

Extending the Langevin model to variable-density pressure-gradient-driven turbulence

We extend the generalized Langevin model, originally developed for the Lagrangian fluid particle velocity in constant-density shear-driven turbulence, to variable-density (VD) pressure-gradient-driven flows. VD effects due to non-uniform mass concentrations (e.g. mixing of different species) are considered. In the extended model large density fluctuations leading to large differential fluid accelerations are accounted for. This is an essential ingredient to represent the strong coupling between the density and velocity fields in VD hydrodynamics driven by active scalar mixing. The small scale anisotropy, a fundamentally "non-Kolmogorovian" feature of pressure-gradient-driven flows, is captured by a tensorial stochastic diffusion term. The extension is so constructed that it reduces to the original Langevin model in the limit of constant density. We show that coupling a Lagrangian mass-density particle model to the proposed extended velocity equation results in a statistical representation of VD turbulence that has important benefits. Namely, the effects of the mass flux and the specific volume, both essential in the prediction of VD flows, are retained in closed form and require no explicit closure assumptions. The paper seeks to describe a theoretical framework necessary for subsequent applications. We derive the rigorous mathematical consequences of assuming a particular functional form of the stochastic momentum equation coupled to the stochastic density field in VD flows. A previous article discussed VD mixing and developed a stochastic Lagrangian model equation for the mass-density. Second in the series, this article develops the momentum equation for VD hydrodynamics. A third, forthcoming paper will combine these ideas on mixing and hydrodynamics into a comprehensive framework: it will specify a model for the coupled problem and validate it by computing a Rayleigh-Taylor flow.Comment: Accepted in Journal of Turbulence, Jan 7, 201