Stock market series analysis using self-organizing maps

In this work a new clustering technique is implemented and tested. The proposed approach is based on the application of a SOM (self-organizing map) neural network and provides means to cluster U-MAT aggregated data. It relies on a flooding algorithm operating on the U-MAT and resorts to the Calinski and Harabask index to assess the depth of flooding, providing an adequate number of clusters. The method is tuned for the analysis of stock market series. Results obtained are promising although limited in scope.Neste trabalho é implementada e testada uma nova técnica de agrupamento. A abordagem proposta baseia-se na aplicação de uma rede neuronal SOM (mapa auto-organizado) e permite agrupar dados sobre a matriz de distancias (U-MAT). É utilizado um algoritmo de alagamento ("flooding") sobre a U-MAT e o índice de Calinski e Harabasz avalia a profundidade do alagamento determinando-se, assim, o número de grupos mais adequado. O método é desenhado especificamente para a análise de séries temporais da bolsa de valores. Os resultados obtidos são promissores, embora se registem ainda limitações

XENO-Free production and recovery of human pluripotent stem cells using synthetic dissolvable microcarriers

The implementation of scalable culture platforms for the large-scale production of human pluripotent stem cells (hPSC) and their derivatives is mandatory to fulfill the requirement of obtaining large numbers of these cells for cell therapies and other in vitro biomedical applications, such as drug screening, toxicology assays and disease modeling. Recent progress includes the development of chemically-defined culture conditions for manufacturing of hPSC and their derivatives, namely the development of xeno-free microcarrier platforms to meet good manufacturing practice (GMP) quality requirements [1]. One challenge that remains to be addressed is the establishment of a robust, scalable, and cost-effective downstream processing for cell recovery and removal of the microcarriers. Since hPSC have the tendency to create multilayers of cells on the microcarriers, often forming very large cell-microcarrier aggregates, the process of cell recovery can be technically challenging and time consuming. In this work, we developed a robust and efficient platform for large-scale production of hPSC using synthetic dissolvable microcarriers, which can be quickly dissolved by a non-proteolytic enzyme. This allows an easy cell recovery without the need of the microcarrier separation step, facilitating the downstream processing. Moreover, these synthetic microcarriers are sterile and ready-to-use, and are functionalized with the Synthemax® surface, based on a peptide-acrylate matrix designed for long-term support of hESC self-renewal [2]. hPSC were able to attach and grow on the dissolvable microcarriers and the expansion process was evaluated in a scalable stirred culture system. The cells growth performance on these microcarriers was comparable with the ones obtained when culturing hPSCs in non-dissolvable microcarriers (backbone of polystyrene coated with different ECM molecules), being possible to obtain 1.3x106 cells/mL during 5 days. Importantly, hPSCs cultured on these novel microcarriers were efficiently recovered without the need of the filtration step to separate the microcarriers from the cells and maintained their typical colony morphology and pluripotency-associated marker-expression after re-plating on tissue culture plates. Moreover, their potential for spontaneous differentiation into cells of the three embryonic germ layers was demonstrated through formation of embryoid bodies containing cells expressing typical markers of endoderm, ectoderm and mesoderm. These novel synthetic dissolvable microcarriers allow an easy and efficient downstream processing for hPSCs recovery after expansion/differentiation, without compromising the quality of the cells (viability, potency and functionality), which are a major process breakthrough for stem cell manufacturing. [1] Badenes SM, et al., “Defined Essential 8™ Medium and Vitronectin Efficiently Support Scalable Xeno-Free Expansion of Human Induced Pluripotent Stem Cells in Stirred Microcarrier Culture Systems”, PlosOne (2016), 11(3):e0151264. [2] Melkoumian Z, et al, “Synthetic peptide-acrylate surfaces for long-term self-renewal and cardiomyocyte differentiation of human embryonic stem cells”, Nat Biotechnol (2010), 28(6): 606-10. Acknowledgements: We acknowledge CORNING Incorporated for supplying the dissolvable microcarriers

Scaling up a chemically-defined aggregate-based suspension culture system for neural commitment of human pluripotent stem cells

The demand of high cell numbers for applications in cellular therapies and drug screening requires the development of scalable platforms capable to generating highly pure populations of tissue-specific cells from human pluripotent stem cells. This work describes the scaling-up of an aggregate-based culture system for neural induction of human induced pluripotent stem cells (hiPSCs) under chemically-defined conditions. Since initial cell density and aggregate size have an important impact in the expansion and commitment of these cells into a particular lineage, a combination of non-enzymatic dissociation and rotary agitation was successfully used to produce homogeneous populations of hiPSC aggregates with an optimal (140 µm) and narrow distribution of diameters (coefficient of variation of 21.6%). Scalable neural commitment of hiPSCs as 3D aggregates was then performed in 50 mL spinner flasks, and process optimization using a factorial design approach was developed involving parameters such as agitation rate and seeding density. We were able to produce neural progenitor cell cultures, that at the end of a 6-day neural induction process contained less than 3% of Oct4-positive cells and that, after replating, retained more than 60% of Pax6-positive neural cells. Furthermore, after scalable differentiation, hiPSC-derived neural progenitors still retained their multipotent potential, being able to give rise to neuronal and glial cells. The results presented in this work should set the stage for the future generation of a clinically relevant number of human neural progenitors for transplantation and other biomedical applications using totally controlled, automated and reproducible large-scale bioreactor culture systems

Reduction of skeletal anomalies in meagre (Argyrosomus regius, Asso, 1801) through early introduction of inert diet

The consolidation of meagre (Argyrosomus regius) in aquaculture requires an understanding and optimization of larval rearing and nutritional conditions. The aim of this study was to analyse the effects of an early introduction of inert diets during larval rearing, on growth performance, digestive enzymes activity and development of skeletal anomalies. This study evaluated the effects of three different timings for the introduction of inert diet during larval rearing: a control group (CTRL) where inert diet was initiated at 14 days after hatching (DAH) and two treatment groups that had an earlier introduction of inert diet at 8 DAH (T1) and 11 DAH (T2). Meagre larvae exhibited similar pancreatic and intestinal enzymatic activities among the different dietary treatments. No differences in the overall prevalence of anomalies were observed between treatments at 25 or 50 DAH, however, a significant reduction was observed in all groups with the transition from larval to juvenile stage. The precocious introduction of inert diet shifted the distribution of vertebral anomalies to a more anterior vertebral column region. Altogether, this study shows that earlier introduction of inert diets in meagre hatcheries can be beneficial for meagre production in aquaculture.info:eu-repo/semantics/publishedVersio

Antimicrobial screening of Plectranthus madagascariensis and P. neochilus extracts

Natural products are widely used as traditional medicines and are a common source of bioactive molecules for the treatment of bacterial infections. In particular, some plants of the genus Plectranthus (Lamiaceae) have demonstrated several applications, including the treatment of various infections. In this work, aqueous, acetonic and methanolic extracts of P. madagascariensis and P. neochilus were prepared using several extraction methods (infusion, decoction, maceration, microwave- and ultrasoundassisted and supercritical fluids). All extracts were screened for their antimicrobial activity against Gram positive bacteria (Enterococcus faecalis, Staphylococcus aureus, Bacillus subtilis and Mycobacterium smegmatis) and Gram negative bacteria (Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli) and two yeast (Candida albicans and Saccharomyces cerevisiae) strains. The P. madagascariensis acetonic extracts obtained using ultrasound and maceration methods and P. neochilus acetonic extract obtained by ultrasound technique showed activity against the five tested Gram positive bacteria (5‒24 mm of inhibition zone using the well diffusion test). The antimicrobial activity was further evaluated by the microdilution method (MIC values were between 250‒0.49 μg/mL) and the bioautography assay against S. aureus. The P. madagascariensis ultrasound acetonic extract was the most active extract against all the tested Gram positive bacteria (MIC values ranged between 31.25 - 0.49 μg/mL). It was also active against resistant MRSA and VRE strains (MIC values ranged between 31.25-0.98 μg/mL). The S. aureus bioautography assay showed that the more polar compounds were the responsible for the antimicrobial activity

Monitoring antibiotic resistance in aquatic environments

info:eu-repo/semantics/publishedVersio

role of female sex hormone receptors

Funding Information: Funding: This study was supported by grant IECT-FAPEMA-05796/18 and FAPEMA IECT 30/2018-IECT Saúde, by the Research Center of the Portuguese Oncology Institute of Porto (project no. PI86-CI-IPOP-66-2017); by European Investment Funds by FEDER/COMPETE/POCI—Operational Competitiveness and Internationalization Program, and national funds by FCT—Portuguese Foundation for Science and Technology under projects UID/AGR/04033/2020, UIDB/CVT/00772/2020 and by Base Funding-UIDB/00511/2020 of the Laboratory for Process Engineering, Environment, Biotechnology, and Energy—LEPABE—funded by national funds through the FCT/MCTES (PID-DAC); Project 2SMART-engineered Smart materials for Smart citizens, with reference NORTE-01-0145-FEDER-000054, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.A growing proportion of oropharyngeal squamous cell carcinomas (OPSCC) are associated with infection by high-risk human papillomavirus (HPV). For reasons that remain largely unknown, HPV+OPSCC is significantly more common in men than in women. This study aims to determine the incidence of OPSCC in male and female HPV16-transgenic mice and to explore the role of female sex hormone receptors in the sexual predisposition for HPV+ OPSCC. The tongues of 30-weeks-old HPV16-transgenic male (n = 80) and female (n = 90) and matched wild-type male (n = 10) and female (n = 10) FVB/n mice were screened histologically for intraepithelial and invasive lesions in 2017 at the Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Por-tugal. Expression of estrogen receptors alpha (ERα) and beta (ERβ), progesterone receptors (PR) and matrix metalloproteinase 2 (MMP2) was studied immunohistochemically. Collagen remodeling was studied using picrosirius red. Female mice showed robust ERα and ERβ expression in intraepithelial and invasive lesions, which was accompanied by strong MMP2 expression and marked collagen remodeling. Male mice showed minimal ERα, ERβ and MMP2 expression and unaltered collagen patterns. These results confirm the association of HPV16 with tongue base cancer in both sexes. The higher cancer incidence in female versus male mice contrasts with data from OPSCC patients and is associated with enhanced ER expression via MMP2 upregulation.publishersversionpublishe

Modeling Rett syndrome with human patient-specific forebrain organoids

Copyright © 2020 Gomes, Fernandes, Vaz, Silva, Bekman, Xapelli, Duarte, Ghazvini, Gribnau, Muotri, Trujillo, Sebastião, Cabral and Diogo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Engineering brain organoids from human induced pluripotent stem cells (hiPSCs) is a powerful tool for modeling brain development and neurological disorders. Rett syndrome (RTT), a rare neurodevelopmental disorder, can greatly benefit from this technology, since it affects multiple neuronal subtypes in forebrain sub-regions. We have established dorsal and ventral forebrain organoids from control and RTT patient-specific hiPSCs recapitulating 3D organization and functional network complexity. Our data revealed a premature development of the deep-cortical layer, associated to the formation of TBR1 and CTIP2 neurons, and a lower expression of neural progenitor/proliferative cells in female RTT dorsal organoids. Moreover, calcium imaging and electrophysiology analysis demonstrated functional defects of RTT neurons. Additionally, assembly of RTT dorsal and ventral organoids revealed impairments of interneuron's migration. Overall, our models provide a better understanding of RTT during early stages of neural development, demonstrating a great potential for personalized diagnosis and drug screening.We also acknowledge financial support from Fundação para a Ciência e a Tecnologia (FCT), Portugal, through iBB, Institute for Bioengineering and Biosciences (UIDB/04565/2020) and from Programa Operacional Regional de Lisboa 2020 (Project No. 007317). AG was supported by FCT (PD/BD/128373/2017).info:eu-repo/semantics/publishedVersio

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe