SARS-CoV-2 virus classification based on stacked sparse autoencoder

Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infection diagnosis, metagenomics, phylogenetics, and analysis. Considering that motivation, the authors proposed an efficient viral genome classifier for the SARS-CoV-2 using the deep neural network based on the stacked sparse autoencoder (SSAE). For the best performance of the model, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a classification of the SARS-CoV-2. For that, a dataset based on k-mers image representation was applied. We performed four experiments to provide different levels of taxonomic classification of the SARS-CoV-2. The SSAE technique provided great performance results in all experiments, achieving classification accuracy between 92% and 100% for the validation set and between 98.9% and 100% when the SARS-CoV-2 samples were applied for the test set. In this work, samples of the SARS-CoV-2 were not used during the training process, only during subsequent tests, in which the model was able to infer the correct classification of the samples in the vast majority of cases. This indicates that our model can be adapted to classify other emerging viruses. Finally, the results indicated the applicability of this deep learning technique in genome classification problems.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) 00

A Novel Deep Neural Network Technique for Drug–Target Interaction

The authors wish to acknowledge the financial support of the CoordenacAo de Aperfeicoamento de Pessoal de Nivel Superior (CAPES). This research was supported by the High-Performance Computing Center at UFRN (NPAD/UFRN). This study was financed in part by the CoordenacAo de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)-Finance Code 001.Drug discovery (DD) is a time-consuming and expensive process. Thus, the industry employs strategies such as drug repositioning and drug repurposing, which allows the application of already approved drugs to treat a di erent disease, as occurred in the first months of 2020, during the COVID-19 pandemic. The prediction of drug–target interactions is an essential part of the DD process because it can accelerate it and reduce the required costs. DTI prediction performed in silico have used approaches based on molecular docking simulations, including similarity-based and network- and graph-based ones. This paper presents MPS2IT-DTI, a DTI prediction model obtained from research conducted in the following steps: the definition of a new method for encoding molecule and protein sequences onto images; the definition of a deep-learning approach based on a convolutional neural network in order to create a new method for DTI prediction. Training results conducted with the Davis and KIBA datasets show that MPS2IT-DTI is viable compared to other state-of-the-art (SOTA) approaches in terms of performance and complexity of the neural network model. With the Davis dataset, we obtained 0.876 for the concordance index and 0.276 for the MSE; with the KIBA dataset, we obtained 0.836 and 0.226 for the concordance index and the MSE, respectively. Moreover, the MPS2IT-DTI model represents molecule and protein sequences as images, instead of treating them as an NLP task, and as such, does not employ an embedding layer, which is present in other models.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) 001High-Performance Computing Center at UFRN (NPAD/UFRN

Hydrogen oxidizing bacteria are capable of removing orthophosphate to ultra-low concentrations in a fed batch reactor configuration

This paper proposes the use of hydrogen oxidizing bacteria (HOB) for the removal of orthophosphate from surface water as treatment step to prevent cyanobacterial blooms. To be effective as an orthophosphate removal strategy, an efficient transfer of hydrogen to the HOB is essential. A trickling filter was selected for this purpose. Using this system, a removal rate of 11.32 +/- 0.43 mg PO4-3-P/L.d was achieved. The HOB biomass, developed on the trickling filter, is composed of 1.25% phosphorus on dry matter, which suggests that the orthophosphate removal principle is based on HOB growth. Cyanobacterial growth assays of the untreated and treated water showed that Synechocystis sp was only able to grow in the untreated water. Orthophosphate was removed to average residual values of 0.008 mg/L. In this proof of principle study, it is shown that HOB are able to remove orthophosphate from water to concentrations that prevent cyanobacterial growth

Safeguarding the microbial water quality from source to tap

Anthropogenic activities and climate change can deteriorate the freshwater quality and stress its availability. This stress can, in turn, have an impact on the biostability of drinking water. Up to now, the microbiological quality of drinking water has been maintained through the selection of high-quality water sources allied to the use of disinfectants and the removal of organic carbon. But as freshwater becomes richer in other nutrients, strategies used so far may not suffice to keep a steady and high-quality supply of drinking water in the future. This article readdresses the discussion on drinking water biostability. We need to reframe the concept as a dynamic equilibrium that considers the available nutrients and energy sources (potential for growth) relative to the abundance and composition of the bacterial community (potential to consume the available resources)

Incidence and anatomic localization of oral candidiasis in patients with AIDS hospitalized in a public hospital in Belo Horizonte, MG, Brazil

The objective of this study was to evaluate the incidence, anatomic localization and yeast species isolated from each clinical type of oral candidiasis. The clinical samples were obtained from 67 patients with AIDS with CD4 cell counts below 200 cells/mm³ and hospitalized in a public hospital (Eduardo de Menezes Hospital) in the city of Belo Horizonte, MG, Brazil. Yeasts were isolated using Chromagar® Candida. The results show that 50.7% of these patients had oral candidiasis. The pseudomembranous form was the most frequent clinical manifestation of oral candidiasis, followed by the erythematous and angular cheilite forms. The most common site of these clinical forms of oral candidiasis was the tongue. Candida albicans was the most common yeast species isolated from the lesions. However, other species were also found to be associated with these forms of oral candidiasis

The Arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates SNF1-related protein kinase 1 (SnRK1) stability

The deposited article is a post-print version and has been submitted to peer review.This publication hasn't any creative commons license associated.This deposit is composed by the main article, and it hasn't any supplementary materials associated.The ability to sense and respond to sugar signals allows plants to cope with environmental and metabolic changes by adjusting growth and development accordingly. We previously reported that the SR45 splicing factor negatively regulates glucose signaling during early seedling development in Arabidopsis thaliana Here, we show that under glucose-fed conditions, the Arabidopsis sr45-1 loss-of-function mutant contains higher amounts of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) despite unaffected SnRK1 transcript levels. In agreement, marker genes for SnRK1 activity are upregulated in sr45-1 plants, and the glucose hypersensitivity of sr45-1 is attenuated by disruption of the SnRK1 gene. Using a high-resolution RT-PCR panel, we found that the sr45-1 mutation broadly targets alternative splicing in vivo, including that of the SR45 pre-mRNA itself. Importantly, the enhanced SnRK1 levels in sr45-1 are suppressed by a proteasome inhibitor, indicating that SR45 promotes targeting of the SnRK1 protein for proteasomal destruction. Finally, we demonstrate that SR45 regulates alternative splicing of the Arabidopsis 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase previously shown to interact with and regulate the stability of SnRK1 in vitro, thus providing a mechanistic link between SR45 function and the modulation of degradation of the SnRK1 energy sensor in response to sugars.Fundação para a Ciência e a Tecnologia grants: (PTDC/BIA-PLA/3937/2012, PTDC/BIA-PLA/1084/2014, SFRH/BPD/80073/2011, SFRH/BPD/94796/2013); EMBO Installation Program: (EMBO-Proj.1984); Scottish Government Rural and Environment Science and Analytical Services (RESAS).info:eu-repo/semantics/publishedVersio

Mesenchymal Stromal Cell Secretome: Influencing Therapeutic Potential by Cellular Pre-conditioning

Mesenchymal stromal cells (MSCs) are self-renewing, culture-expandable adult stem cells that have been isolated from a variety of tissues, and possess multipotent differentiation capacity, immunomodulatory properties, and are relatively non-immunogenic. Due to this unique set of characteristics, these cells have attracted great interest in the field of regenerative medicine and have been shown to possess pronounced therapeutic potential in many different pathologies. MSCs' mode of action involves a strong paracrine component resulting from the high levels of bioactive molecules they secrete in response to the local microenvironment. For this reason, MSCs' secretome is currently being explored in several clinical contexts, either using MSC-conditioned media (CM) or purified MSC-derived extracellular vesicles (EVs) to modulate tissue response to a wide array of injuries. Rather than being a constant mixture of molecular factors, MSCs' secretome is known to be dependent on the diverse stimuli present in the microenvironment that MSCs encounter. As such, the composition of the MSCs' secretome can be modulated by preconditioning the MSCs during in vitro culture. This manuscript reviews the existent literature on how preconditioning of MSCs affects the therapeutic potential of their secretome, focusing on MSCs' immunomodulatory and regenerative features, thereby providing new insights for the therapeutic use of MSCs' secretome

Preparation, Characterization and Effectiveness to Delay Lipid Oxidation in Almonds and Beef Meat

Funding Information: This study was carried out under the VIPACFood project, funded by ARIMNet2 (Coordination of Agricultural Research in the Mediterranean; 2014–2017), an ERA-NET Action financed by the European Union under the Seventh Framework Programme, and by the Programa de Cooperación Interreg V-A España–Portugal (POCTEP) 2014–2020 (project 0377_IBERPHENOL_6_E). Cássia H. Barbosa is grateful for her research grant in the frame of the VIPACFood project (ARIMNET2/0003/2016) and the Foundation for Science and Technology (FCT), Portugal, for the Ph.D. grant 2021.08154.BD. This research was also funded by PT national funds (FCT/MCTES, Fundação para a Ciência e Tecnologia and Ministério da Ciência, Tecnologia e Ensino Superior) through grants UIDB/50006/2020 and UIDB/00211/2020. L. Barbosa-Pereira is grateful to the Spanish Ministry of Science, Innovation and Universities for her “Juan de la Cierva-Incorporación” grant (Agreement No. IJCI-2017-31665). Publisher Copyright: © 2023 by the authors.Low-density polyethylene-based packaging with 4% lemon extract (LDPE/4LE) and two polylactic-based (PLA) packaging materials with 4% and 6% lemon extract (PLA/PEG/4LE and PLA/6LE) were produced. O2 and water permeability tests were performed, the total and individual phenolic compounds content were measured, and the films’ antioxidant activities were determined. The films’ ability to delay lipid oxidation was tested in two model foods: almonds, packaged with LDPE/4LE, PLA/4LE and PLA/6LE for a maximum period of 60 days at 40 °C (accelerated assay); and beef meat, packaged with the PLA/6LE for a maximum period of 11 days at 4 °C. The LE improved the WVP in all of the active films by 33%, 20% and 60% for the LDPE/4LE, PLA/4LE and PLA/6LE films, respectively. At the end of 10 days, the migration of phenolic compounds through the PLA films was measured to be 142.27 and 114.9 μg/dm2 for the PLA/4LE and PLA/6LE films, respectively, and was significantly higher than phenolic compounds migration measured for the LDPE/4LE (15.97 μg/dm2). Naringenin, apigenin, ferulic acid, eriocitrin, hesperidin and 4-hydroxybenzoic acid were the main identified compounds in the PLA, but only 4-hydroxybenzoic acid, naringenin and p-coumaric acid were identified in the LDPE films. Regarding the films’ ability to delay lipid oxidation, LDPE/4LE presented the best results, showing a capacity to delay lipid oxidation in almonds for 30 days. When applied to raw beef meat, the PLA/6LE packaging was able to significantly inhibit lipid oxidation for 6 days, and successfully inhibited total microorganisms’ growth until the 8th day of storage.publishersversionpublishe

Urinary incontinence related to perineal muscle strength in the first trimester of pregnancy: cross-sectional study

Objective To analyze pelvic floor muscle strength (PFMS), urinary continence and quality of life related to urinary incontinence (UI) of women in the first trimester of pregnancy. Method Cross-sectional study with a sample of 500 women who started prenatal care in a complementary healthcare facility in Guarulhos, state of São Paulo, from 2012 and 2013. Pelvic floor muscle strength was evaluated through perineometry. The pregnant women who presented UI answered the International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF). Results It was found that maternal age (OR=1.06; CI95% 1.02-1.11) and prior UI (OR=15.12; 95%CI 8.19-27.92) are the variables that, in tandem, best explain the occurrence of UI at the beginning of pregnancy. The mean score on the ICIQ-SF was 8.2 (SD=3.9), considered a moderate impact on quality of life. Conclusion Older pregnant women with prior UI are more likely to have UI in the first trimester of pregnancy.
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