GTO : A toolkit to unify pipelines in genomic and proteomic research

Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics enquiry to students in life sciences. GTO is implemented in C language and is available, under the MIT license, at https://bioinformatics.ua.pt/gto. (C) 2020 The Authors. Published by Elsevier B.V.Peer reviewe

Evidence of Genetic Segregation among Meagre (Argyrosomus regius) Atlantic Spawning Areas

The meagre Argyrosomus regius, one of the largest sciaenidae in the world, is a valuable resource for fisheries and aquaculture. Despite its socioeconomic relevance, knowledge about population dynamics and wild stocks is still scarce, and conservation risks are associated with overexploitation. Two genetic distinct groups, one in the North Atlantic Ocean and one in the eastern Mediterranean Sea, were identified by previous studies. However, little is known about the genetic structure of the Atlantic group, where four important spawning areas have been identified. To assess if each spawning area is an independent breeding unit, the genetic diversity, populational structure, and demographic history of A. regius along the North-East and Eastern Central Atlantic coast were analyzed, using 15 microsatellite loci. Results corroborate the hypothesis tested, suggesting four genetic groups: a first group encompassing individuals from the Gironde spawning area, a second group encompassing individuals from the Tagus spawning area, a third group corresponding to individuals captured in the Algarve region, and a forth group gathering individuals from Morocco and Mauritania. This study reveals the need for specific fisheries management plans considering genetic structure information, and highlights the need for international cooperation

Draft genome sequence of multitrait plant growth-promoting Bacillus sp. strain RZ2MS9

Plant growth-promoting rhizobacteria (PGPR) are able to colonize plant rhizosphere and improve plant growth through several direct and indirect mechanisms (1), which makes them good candidates for use as biofertilizers. Members of the genus Bacillus are often reported as PGPR because of multiple traits that promote plant growth, for instance, the ability to fix nitrogen (2), produce hormones like indole acetic-acid (IAA), solubilize phosphate, and suppress pathogen growth (3). The rhizobacterium Bacillus sp. strain RZ2MS9 was isolated in Brazil from the rhizosphere of guarana, a typical tropical plant, and was identified as Bacillus thuringiensis by multi-locus sequence type (MLST) analysis. On in vitro tests, this strain was able to produce 67.40 _g IAA/ml, solubilize phosphate, produce siderophore, and fix nitrogen. The strain promoted the growth of maize (Zea mays) and soybean (Glycine max) in an experiment conducted in greenhouse conditions, suggesting that it can be used in a broad range of hosts, which is a greatly desired feature in biofertilizer development (B. D. Batista, submitted for publication). The draft genome sequence of the strain presented here will be useful to explore its genomic features as a multitrait PGPR

Sutureless bioprosthesis for aortic valve replacement: surgical and clinical outcomes

© 2022 The Authors. Journal of Cardiac Surgery published by Wiley Periodicals LLC. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.Background: Aortic valve stenosis is the most common adult valve disease in industrialized countries. The aging population and the increase in comorbidities urge the development of safer alternatives to the current surgical treatment. Sutureless bioprosthesis has shown promising results, especially in complex procedures and in patients requiring concomitant surgeries. Objectives: Assess the clinical and hemodynamic performance, safety, and durability of the Perceval® prosthetic valve. Methods: This single-center retrospective longitudinal cohort study collected data from all adult patients with aortic valve disease who underwent aortic valve replacement with a Perceval® prosthetic valve between February 2015 and October 2020. Of the 196 patients included (mean age 77.20 ± 5.08 years; 45.4% female; mean EuroSCORE II 2.91 ± 2.20%), the majority had aortic stenosis. Results: Overall mean cross-clamp and cardiopulmonary bypass times were 33.31 ± 14.09 min and 45.55 ± 19.04 min, respectively. Mean intensive care unit and hospital stay were 3.32 ± 3.24 days and 7.70 ± 5.82 days, respectively. Procedural success was 98.99%, as two explants occurred. Four valves were reimplanted due to intraoperative misplacement. Mean transvalvular gradients were 7.82 ± 3.62 mmHg. Pacemaker implantation occurred in 12.8% of patients, new-onset atrial fibrillation in 21.9% and renal replacement support was necessary for 3.1%. Early mortality was 2.0%. We report no structural valve deterioration, strokes, or endocarditis, and one successfully treated valve thrombosis. Conclusions: Our study confirms the excellent clinical and hemodynamic performance and safety of a truly sutureless aortic valve, up to a 5-year follow-up. These results were consistent in isolated and concomitant interventions, solidifying this device as a viable option for the treatment of isolated aortic valve disease.info:eu-repo/semantics/publishedVersio

Public awareness and engagement in relation to the coastal oil spill in northeast Brazil

Social media data is a rich source of information to assess human activities in catastrophic events. Here, we use social media data to understand how the 2019 Brazilian oil spill influenced social attitudes. Data were collected from the globally popular Instagram platform between August 1, 2019 and March 1, 2020. First, we manually identified the 5 most popular (portuguese language) hashtags related to the oil spill #oleonononordeste;#desastreambiental;#ma rsemoleo;#sosnordeste;#ma rsempetroleo. In the sequence, we collected information on captions, post metadata and users associated with posts retrieved using the selected hashtags. We identified a total of 7,413 posts. These posts were grouped in topics: government (47.76%), protest (24.37%), volunteers (24.45%), biodiversity (0.003%), origin (0.006%), tourism (0.008%) and others (0.016%). All topics had the peak of posts in October and November 2019. Nevertheless, interest in the oil spill was temporary, with most posts appearing in the 2-4 months after the beginning of the disaster. Our findings illustrate the enormous potential of using social media data for understanding and monitoring human engagement with environmental disasters, but also suggest that conservationists and environmental groups may only have a limited 'window of opportunity' to engage and mobilize public support for remediation and restoration efforts.Peer reviewe

Synthesis, characterization, antibacterial and antitumoral activities of mononuclear zinc complexes containing tridentate amine based ligands with N3 or N2O donor groups

The synthesis and characterization of the four zinc(II) complexes [Zn(HL1)Cl-2] (1), [Zn(H2L2)Cl-2](2), [Zn(H2L3)Cl-2] (3) and[Zn(H2L4)Cl-2] (4), where HL1 = (bis-2-pyridylmethyl)amine, H2L2 = (2-hydroxybenzyl- 2-pyridylmethyl) amine, H2L3 = N-2[(pyridine-2-ylmethyl)amino)ethanol, H2L4 = 1-[(pyridine-2-ylmethyl)- amino]-propan-2-ol are reported; (3) and (4) are new while (2) was reported previously but its structure had not been determined. The complexes were characterized by elemental analysis, IR, UV-Vis and NMR spectroscopic, electrospray ionization mass spectrometry (ESI(+)-MS) and tandem mass spectrometry ESI(+)-MS/MS). X-ray diffraction studies were performed for complexes (1)-(3) revealing the presence of mononuclear structures in the solid state. The X-ray analyses of (1) and (3) demonstrate that HL1 and HL2 act as tridentate ligands, while the ligand H2L2 in (2) is bidentate. The cytotoxic properties of the ligands and of all the complexes were examined using human leukemia THP-1, U937 and Molt-4 cells. Complex (4) exhibited the highest cytotoxicity in this series with an IC50 value of 75 +/- 1 mu mol L (1) against U937 cells. Transmission electron microscopy (TEM) reveals ultrastructural changes typical of apoptotic cells. The induction of apoptosis was confirmed by the annexin V assay. The antimicrobial activity of complexes (1)-(4) was also investigated in vitro against four Gram-positive bacteria (ATCC10832, ATCC25923, COL) and the clinical Staphylococcus aureus isolate LSA88 (SEC/SEF/ TSST-1+). Complex (2) showed the most potent inhibitory activity, reaching almost 100% of inhibition against all strains tested. Morphological investigations using TEM indicate that the antibacterial activity of complex (2) may be associated with the inhibition of cell wall and therefore cell division. (C) 2014 Elsevier B. V. All rights reserved

The CMS Electromagnetic Calorimeter Data Acquisition System at the 2006 Test Beam

The Electromagnetic Calorimeter of the CMS experiment at the CERN LHC is an homogeneous calorimeter made of about 80000 Lead Tungstate crystals. From June to November 2006, eleven barrel Supermodules (1700 crystals each) were exposed to beam at CERN SPS, both in stand-alone and in association with portions of the Hadron Calorimeter. We present the description of the system used to configure and readout the calorimeter during this period. The full set of final readout electronics boards was employed, together with the pre-series version of the data acquisition software. During this testbeam, the hardware and software concepts for the final system were validated and the successfull operation of all the ten supermodules was ensured