Moara: a Java library for extracting and normalizing gene and protein mentions

<p>Abstract</p> <p>Background</p> <p>Gene/protein recognition and normalization are important preliminary steps for many biological text mining tasks, such as information retrieval, protein-protein interactions, and extraction of semantic information, among others. Despite dedication to these problems and effective solutions being reported, easily integrated tools to perform these tasks are not readily available.</p> <p>Results</p> <p>This study proposes a versatile and trainable Java library that implements gene/protein tagger and normalization steps based on machine learning approaches. The system has been trained for several model organisms and corpora but can be expanded to support new organisms and documents.</p> <p>Conclusions</p> <p>Moara is a flexible, trainable and open-source system that is not specifically orientated to any organism and therefore does not requires specific tuning in the algorithms or dictionaries utilized. Moara can be used as a stand-alone application or can be incorporated in the workflow of a more general text mining system.</p

Marine natural products as innovative cosmetic ingredients

Over the course of the last 20 years, numerous studies have identified the benefits of an array of marine natural ingredients for cosmetic purposes, as they present unique characteristics not found in terrestrial organisms. Consequently, several marine-based ingredients and bioactive compounds are under development, used or considered for skin care and cosmetics. Despite the multitude of cosmetics based on marine sources, only a small proportion of their full potential has been exploited. Many cosmetic industries have turned their attention to the sea to obtain innovative marine-derived compounds for cosmetics, but further research is needed to determine and elucidate the benefits. This review gathers information on the main biological targets for cosmetic ingredients, different classes of marine natural products of interest for cosmetic applications, and the organisms from which such products can be sourced. Although organisms from different phyla present different and varied bioactivities, the algae phylum seems to be the most promising for cosmetic applications, presenting compounds of many classes. In fact, some of these compounds present higher bioactivities than their commercialized counterparts, demonstrating the potential presented by marine-derived compounds for cosmetic applications (i.e., Mycosporine-like amino acids and terpenoids’ antioxidant activity). This review also summarizes the major challenges and opportunities faced by marine-derived cosmetic ingredients to successfully reach the market. As a future perspective, we consider that fruitful cooperation among academics and cosmetic industries could lead to a more sustainable market through responsible sourcing of ingredients, implementing ecological manufacturing processes, and experimenting with inventive recycling and reuse programs.LA/P/0101/2020; SFRH/BD/05377/2021info:eu-repo/semantics/publishedVersio

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite

Asterias (http://www.asterias.info) is an open-source, web-based, suite for the analysis of gene expression and aCGH data. Asterias implements validated statistical methods, and most of the applications use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. These applications cover from array normalization to imputation and preprocessing, differential gene expression analysis, class and survival prediction and aCGH analysis. The source code is available, allowing for extention and reuse of the software. The links and analysis of additional functional information, parallelization of computation and open-source availability of the code make Asterias a unique suite that can exploit features specific to web-based environments

Science communication in bioengineering and biotechnology: Active and collaborative learning project

In a society increasingly dependent on science and technology, the need to equip our students with the most varied digital and communication skills is crucial. Active and collaborative learning among peers is essential for the acquisition of transversal skills. Communication is one of the main tools that the Engineer uses to reach his target audience. Science Communication in Bioengineering and Biotechnology (CCBioTec) is a project on Innovation and Development of Teaching and Learning supported by Center IDEA-UMinho, a structure that emerges to promote and value Innovation and Development of Teaching and Learning at the University of Minho. CCBioTec is transversal to a set of Learning Units (LU) under the responsibility of the Department of Biological Engineering (DEB), including one LU of each year of the Integrated Masters in Biological Engineering and in Biomedical Engineering. The main goals of CCBioTEc are: to foster the awareness of the DEB educational community on the importance of science communication, as well as to develop science communication skills, through the production of short videos (pitches) displaying the explanation, in a simple and dynamic way, of complex concepts of Bioengineering and Biotechnology related with the curricula of each LU. CCBioTec started in the second semester of 2020/21, and it will go on in the 1st semester of 2021/22. The project was designed to be implemented according to the following steps: 1 - Technical and pedagogical training of teachers; 2 - Technical training of students involved in the project - Week CCBioTEC-2021; 3 - Development of materials for Science Communication in Bioengineering and Biotechnology; 4 - CCBioTec-2021 competition. In CCBioTec, teachers presenting himself as a mediator/facilitator of learning, boosting students development of transversal skills, collaborative work, decision making and the expression of ideas, together with the acquisition of knowledge foreseen in the curricular contents of the LU.(undefined)info:eu-repo/semantics/publishedVersio

Synergism in the antibacterial action of ternary mixtures involving silver nanoparticles, chitosan and antibiotics

The investigations of the antibacterial actions, observed in ternary associations involving silver nanoparticles (AgNPs), chitosan and the antibiotics azithromycin (AZ), levofloxacin (LE) or tetracycline (TE), against Gram-negative and Gram-positive bacterial strains, were performed by in vitro antimicrobial susceptibility testing and checkerboard assays. The pH impact in the culture medium was carefully discarded, but preserving the best conditions for solubilizing chitosan. The synergistic antibacterial effects were observed in the most combinations of AgNPs, chitosan and antibiotic, leading to a reduction from 37 to 97% in the minimum inhibitory concentration of the drugs. The mechanisms for the enhanced antimicrobial effects were proposed based on the investigations of the adsorptions of the drugs on the silver surfaces through surface-enhanced Raman scattering (SERS) spectroscopy.

Infrared spectroscopy to assess manufacturing procedures of bone artefacts from the chalcolithic settlement of Vila Nova de São Pedro (Portugal)

Vibrational spectroscopy was applied to study cylindrical engraved bone boxes from the Chalcolithic settlement of Vila Nova de São Pedro (VNSP, Azambuja, Portugal) which has the largest and richest artefact assemblage of Copper Age Western Iberia. The objectives were to reconstitute manufacturing techniques, determine the role of pyrotechnology in the production of cylindrical engraved bone boxes and assess oxygen conditions during burning. Four fragments of cylindrical engraved bone “boxes” from VNSP were used in this research. Anaerobic experimental burn conditions were recreated by using a home-made steel airtight chamber under vacuum. Human bone fragments were burnt at 400–1000 °C for 120–211 min. Fourier-transform infrared spectroscopy analyses were performed on bone powder samples. The resulting spectra and chemometric indices were used as a reference to establish comparisons with the archaeological artefacts. None of these presented spectral features compatible with anaerobic burning. Therefore, aerobic burns were used to achieve the whitish look and were most probably used to attain the darker shade displayed by the artefacts. Artefact manufacturing appears to have relied on bone cutting, bone engraving and maybe polishing, followed by heat treatment. The population from VNSP appears to have been highly specialized in the use of fire to work different raw materials.info:eu-repo/semantics/publishedVersio

LPS Induces mTORC1 and mTORC2 Activation During Monocyte Adhesion

Monocyte adhesion is a crucial step in transmigration and can be induced by lipopolysaccharide (LPS). Here, we studied the role of mammalian target of rapamycin (mTOR) complexes, mTORC1 and mTORC2, and PKC in this process. We used THP-1 cells, a human monocytic cell line, to investigate monocyte adhesion under static and flow conditions. We observed that 1.0 μg/mL LPS increased PI3K/mTORC2 pathway and PKC activity after 1 h of incubation. WYE-354 10−6 M (mTORC2/mTORC1 inhibitor) and 10−6 M wortmannin avoided monocyte adhesion in culture plates. In addition, WYE also blocked LPS-induced CD11a expression. Interestingly, rapamycin and WYE-354 blocked both LPS-induced monocyte adhesion in a cell monolayer and actin cytoskeleton rearrangement, confirming mTORC1 involvement in this process. Once activated, PKC activates mTORC1/S6K pathway in a similar effect observed to LPS. Activation of the mTORC1/S6K pathway was attenuated by 10−6 M U0126, an MEK/ERK inhibitor, and 10−6 M calphostin C, a PKC inhibitor, indicating that the MEK/ERK/TSC2 axis acts as a mediator. In agreement, 80 nM PMA (a PKC activator) mimicked the effect of LPS on the activation of the MEK/ERK/TSC2/mTORC1/S6K pathway, monocyte adhesion to ECV cells and actin cytoskeleton rearrangement. Our findings show that LPS induces activation of mTOR complexes. This signaling pathway led to integrin expression and cytoskeleton rearrangement resulting in monocyte adhesion. These results describe a new molecular mechanism involved in monocyte adhesion in immune-based diseases

Zeolite structures loading with an anticancer compound as drug delivery systems

The authors are thankful to Dr. A. S. Azevedo for collecting the powder diffraction data.Two different structures of zeolites, faujasite (FAU) and Linde type A (LTA), were studied to investigate their suitability for drug delivery systems (DDS). The zeolites in the sodium form (NaY and NaA) were used as hosts for encapsulation of α-cyano-4- hydroxycinnamic acid (CHC). CHC, an experimental anticancer drug, was encapsulated in both zeolites by diffusion in liquid phase. These new drug delivery systems, CHC@zeolite, were characterized by spectroscopic techniques (FTIR, 1H NMR, 13C and 27Al solidstate MAS NMR, and UV−vis), chemical analysis, powder X-ray diffraction (XRD) and scanning electron microscopy (SEM). The effect of the zeolites and CHC@zeolite drug deliveries on HCT-15 human colon carcinoma cell line viability was evaluated. Both zeolites alone revealed no toxicity to HCT-15 cancer cells. Importantly, CHC@zeolite exhibit an inhibition of cell viability up to 585-fold, when compared to the non-encapsulated drug. These results indicate the potential of the zeolites for drug loading and delivery into cancer cells to induce cell deathO.M. and R.A. are recipients of fellowships (SFRH/BD/36463/2007, SFRH/BI/51118/2010) from Fundação para a Ciência e a Tecnologia (FCT, Portugal). This work was supported by the FCT projects refs PEst-C/ QUI/UI0686/2011, PEst-C/CTM/LA0011/2011, and PTDC/ SAU-FCF/104347/2008, under the scope of “Programa Operacional Temático Factores de Competitividade” (COMPETE) of “Quadro Comunitário de Apoio III” and cofinanced by Fundo Comunitário Europeu FEDER, and the Centre of Chemistry and Life and Health Sciences Research Institute (University of Minho, Portugal)