The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org

The Sound Emission Board of the KM3NeT Acoustic Positioning System

We describe the sound emission board proposed for installation in the acoustic positioning system of the future KM3NeT underwater neutrino telescope. The KM3NeT European consortium aims to build a multi-cubic kilometre underwater neutrino telescope in the deep Mediterranean Sea. In this kind of telescope the mechanical structures holding the optical sensors, which detect the Cherenkov radiation produced by muons emanating from neutrino interactions, are not completely rigid and can move up to dozens of meters in undersea currents. Knowledge of the position of the optical sensors to an accuracy of about 10 cm is needed for adequate muon track reconstruction. A positioning system based on the acoustic triangulation of sound transit time differences between fixed seabed emitters and receiving hydrophones attached to the kilometre-scale vertical flexible structures carrying the optical sensors is being developed. In this paper, we describe the sound emission board developed in the framework of KM3NeT project, which is totally adapted to the chosen FFR SX30 ultrasonic transducer and fulfils the requirements imposed by the collaboration in terms of cost, high reliability, low power consumption, high acoustic emission power for short signals, low intrinsic noise and capacity to use arbitrary signals in emission mode.Comment: 9 pages, 4 figure

Novel therapeutic approaches targeting the renin angiotensin system and associated peptides in hypertension and heart failure

Despite the success of renin-angiotensin system (RAS) blockade by angiotensin-converting enzyme (ACE) inhibitors and angiotensin II type 1 receptor (AT1R) blockers, current therapies for hypertension and related cardiovascular diseases are still inadequate. Identification of additional components of the RAS and associated vasoactive pathways, as well as new structural and functional insights into established targets, have led to novel therapeutic approaches with the potential to provide improved cardiovascular protection and better blood pressure control and/or reduced adverse side effects. The simultaneous modulation of several neurohumoral mediators in key interconnected blood pressure–regulating pathways has been an attractive approach to improve treatment efficacy, and several novel approaches involve combination therapy or dual-acting agents. In addition, increased understanding of the complexity of the RAS has led to novel approaches aimed at upregulating the ACE2/angiotensin-(1-7)/Mas axis to counter-regulate the harmful effects of the ACE/angiotensin II/angiotensin III/AT1R axis. These advances have opened new avenues for the development of novel drugs targeting the RAS to better treat hypertension and heart failure. Here we focus on new therapies in preclinical and early clinical stages of development, including novel small molecule inhibitors and receptor agonists/antagonists, less conventional strategies such as gene therapy to suppress angiotensinogen at the RNA level, recombinant ACE2 protein, and novel bispecific designer peptides

A finite element-based machine learning approach for modeling the mechanical behavior of the breast tissues under compression in real-time

[EN] This work presents a data-driven method to simulate, in real-time, the biomechanical behavior of the breast tissues in some image-guided interventions such as biopsies or radiotherapy dose delivery as well as to speed up multimodal registration algorithms. Ten real breasts were used for this work. Their deformation due to the displacement of two compression plates was simulated off-line using the finite element (FE) method. Three machine learning models were trained with the data from those simulations. Then, they were used to predict in real-time the deformation of the breast tissues during the compression. The models were a decision tree and two tree-based ensemble methods (extremely randomized trees and random forest). Two different experimental setups were designed to validate and study the performance of these models under different conditions. The mean 3D Euclidean distance between nodes predicted by the models and those extracted from the FE simulations was calculated to assess the performance of the models in the validation set. The experiments proved that extremely randomized trees performed better than the other two models. The mean error committed by the three models in the prediction of the nodal displacements was under 2 man, a threshold usually set for clinical applications. The time needed for breast compression prediction is sufficiently short to allow its use in real-time (< 0.2 s).This work has been funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through research projects TIN2014-52033-R and DPI2013-40859-R with the support of European FEDER funds.Martínez Martínez, F.; Rupérez Moreno, MJ.; Martínez-Sober, M.; Solves Llorens, JA.; Lorente, D.; Serrano-Lopez, A.; Martinez-Sanchis, S.... (2017). A finite element-based machine learning approach for modeling the mechanical behavior of the breast tissues under compression in real-time. Computers in Biology and Medicine. 90:116-124. https://doi.org/10.1016/j.compbiomed.2017.09.019S1161249

Descriptive analyses of maternally-derived antibody levels against porcine circovirus 2 (PCV-2) in 3- and 21-day-old piglets from farms of four European countries using different vaccination protocols in sows

Background Up to now, information on the levels of maternally-derived antibodies (MDA) against PCV-2 in suckling piglets born to sows vaccinated with different strategies is scarce in the literature. In the present observational study, the PCV-2-specific MDA titres from piglets from 109 farms (thirty 3-day-old and thirty 21-day-old piglets per farm) across four different European countries (France n = 30, Germany n = 27, Italy n = 22 and Spain n = 30) using different sow vaccination strategies (during gestation, as a gilt, as a piglet or never) were assessed. Results In all four countries, mean log PCV-2 MDA titres were higher in 3-day-old piglets than in the 3-week-old ones, being significant in most of all the comparisons performed. Within each country, the highest PCV-2-specific MDA titres were observed in the 3-day-old piglets born to sows vaccinated during gestation. Indeed, in the four countries, more than 60% of this subpopulation (3-day-old piglets from sows vaccinated during pregnancy) had the highest log PCV-2 titres detectable with the ELISA technique used in this study. The lowest MDA titres were more variable. Whereas in France and Germany the lowest titres corresponded to 21-day-old piglets born from sows vaccinated as a piglet, in Italy, they corresponded to 21-day-old piglets derived from sows vaccinated as a gilt and in Spain to 21-day-old piglets born from non-vaccinated sows. In this study, PCV-2-specific MDA titres at 3 and 21 days of age were not affected by sow parity. Conclusions Data obtained could be considered as a European global overview of PCV-2-specific MDA titres present in the pre-vaccinated piglet populations in different European countries, with titres tending to be higher in younger piglets, but with values variable among countries and sow vaccination strategies

Descriptive analyses of maternally-derived antibody levels against porcine circovirus 2 (PCV-2) in 3-and 21-day-old piglets from farms of four European countries using different vaccination protocols in sows

Background Up to now, information on the levels of maternally-derived antibodies (MDA) against PCV-2 in suckling piglets born to sows vaccinated with different strategies is scarce in the literature. In the present observational study, the PCV-2-specific MDA titres from piglets from 109 farms (thirty 3-day-old and thirty 21-day-old piglets per farm) across four different European countries (France n = 30, Germany n = 27, Italy n = 22 and Spain n = 30) using different sow vaccination strategies (during gestation, as a gilt, as a piglet or never) were assessed. Results In all four countries, mean log PCV-2 MDA titres were higher in 3-day-old piglets than in the 3-week-old ones, being significant in most of all the comparisons performed. Within each country, the highest PCV-2-specific MDA titres were observed in the 3-day-old piglets born to sows vaccinated during gestation. Indeed, in the four countries, more than 60% of this subpopulation (3-day-old piglets from sows vaccinated during pregnancy) had the highest log PCV-2 titres detectable with the ELISA technique used in this study. The lowest MDA titres were more variable. Whereas in France and Germany the lowest titres corresponded to 21-day-old piglets born from sows vaccinated as a piglet, in Italy, they corresponded to 21-day-old piglets derived from sows vaccinated as a gilt and in Spain to 21-day-old piglets born from non-vaccinated sows. In this study, PCV-2-specific MDA titres at 3 and 21 days of age were not affected by sow parity. Conclusions Data obtained could be considered as a European global overview of PCV-2-specific MDA titres present in the pre-vaccinated piglet populations in different European countries, with titres tending to be higher in younger piglets, but with values variable among countries and sow vaccination strategies.info:eu-repo/semantics/publishedVersio

Comparison of Mycoplasma hyopneumoniae and porcine circovirus 2 commercial vaccines efficacy when applied separate or combined under experimental conditions

Background Mycoplasma hyopneumoniae (Mhyo) and Porcine circovirus 2 (PCV-2) are two of the most significant infectious agents causing economic losses in the weaning to slaughter period. Due to their similar vaccination age, the objective of this study was to assess the efficacy of two already existing Mhyo (Hyogen®) and PCV-2 (Circovac®) vaccines when administered separately or combined (RTM) by means of Mhyo or PCV-2 experimental challenges. Results Seven groups of animals were included in the study, being three of them challenged with PCV-2, three with Mhyo and one composed of non-challenged, non-vaccinated pigs. Within each experimental challenge, non-vaccinated (NV) groups were compared with double vaccinated groups using the commercial products separated (VS) or combined (VC). Both vaccinated groups showed significant differences for most parameters measured regarding PCV-2 (serology, percentage of infected animals and viral load in tissues) and Mhyo (serology and gross lesions) when compared to NV groups. VS and VC offered similar results, being only significantly different the PCV-2 antibody values at different time points (higher in the VS group) of the study, although not at the termination day (21 days post-PCV-2 inoculation). Conclusion The present study expands the knowledge on the possibility of using two separate Mhyo and PCV-2 commercial vaccines as a RTM product, which offered equivalent virological, immunological and pathological outcomes as compared to these vaccines when used by separate.info:eu-repo/semantics/publishedVersio