•COVID-19 identification in chest X-ray using multi-class and hierarchical learners.•Using a database that reflects a real world scenario with its natural imbalance.•Exploring the textural content ...from the chest X-ray images with pneumonia.•Evaluating handcrafted and learned features to investigate its complementarities.
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Background and Objective:The COVID-19 can cause severe pneumonia and is estimated to have a high impact on the healthcare system. Early diagnosis is crucial for correct treatment in order to possibly reduce the stress in the healthcare system. The standard image diagnosis tests for pneumonia are chest X-ray (CXR) and computed tomography (CT) scan. Although CT scan is the gold standard, CXR are still useful because it is cheaper, faster and more widespread. This study aims to identify pneumonia caused by COVID-19 from other types and also healthy lungs using only CXR images.
Methods:In order to achieve the objectives, we have proposed a classification schema considering the following perspectives: i) a multi-class classification; ii) hierarchical classification, since pneumonia can be structured as a hierarchy. Given the natural data imbalance in this domain, we also proposed the use of resampling algorithms in the schema in order to re-balance the classes distribution. We observed that, texture is one of the main visual attributes of CXR images, our classification schema extract features using some well-known texture descriptors and also using a pre-trained CNN model. We also explored early and late fusion techniques in the schema in order to leverage the strength of multiple texture descriptors and base classifiers at once.
To evaluate the approach, we composed a database, named RYDLS-20, containing CXR images of pneumonia caused by different pathogens as well as CXR images of healthy lungs. The classes distribution follows a real-world scenario in which some pathogens are more common than others.
Results:The proposed approach tested in RYDLS-20 achieved a macro-avg F1-Score of 0.65 using a multi-class approach and a F1-Score of 0.89 for the COVID-19 identification in the hierarchical classification scenario.
Conclusions:As far as we know, the top identification rate obtained in this paper is the best nominal rate obtained for COVID-19 identification in an unbalanced environment with more than three classes. We must also highlight the novel proposed hierarchical classification approach for this task, which considers the types of pneumonia caused by the different pathogens and lead us to the best COVID-19 recognition rate obtained here.
The long-range and short-range WindScanner systems (LRWS and SRWS), multi-Doppler lidar instruments, when combined together can map the turbulent flow around a wind turbine and at the same time ...measure mean flow conditions over an entire region such as a wind farm. As the WindScanner technology is novel, performing field campaigns with the WindScanner systems requires a methodology that will maximize the benefits of conducting WindScanner-based experiments. Such a methodology, made up of 10 steps, is presented and discussed through its application in a pilot experiment that took place in a complex and forested site in Portugal, where for the first time the two WindScanner systems operated simultaneously. Overall, this resulted in a detailed site selection criteria, a well-thought-out experiment layout, novel flow mapping methods and high-quality flow observations, all of which are presented in this paper.
Marine organisms represent almost half of total biodiversity and are a very important source of new bioactive substances. Within the varied biological activities found in marine products, their ...antimicrobial activity is one of the most relevant. Infectious diseases are responsible for high levels of morbidity and mortality and many antimicrobials lose their effectiveness with time due to the development of resistance. These facts justify the high importance of finding new, effective and safe anti-infective agents. Among the variety of biological activities of marine xanthone derivatives, one that must be highlighted is their anti-infective properties. In this work, a literature review of marine xanthones with anti-infective activity, namely antibacterial, antifungal, antiparasitic and antiviral, is presented. Their structures, biological activity, sources and the methods used for bioactivity evaluation are described. The xanthone derivatives are grouped in three sets: xanthones, hydroxanthones and glycosylated derivatives. Moreover, molecular descriptors, biophysico-chemical properties, and pharmacokinetic parameters were calculated, and the chemical space occupied by marine xanthone derivatives is recognized. The chemical space was compared with marketed drugs and framed accordingly to the drug-likeness concept in order to profile the pharmacokinetic of anti-infective marine xanthone derivatives.
Recent evidence supports the influence of neuroimmune system activation on behavior. We have demonstrated that ethanol activates the innate immune system by stimulating toll-like receptor 4 (TLR4) ...signaling in glial cells, which triggers the release of inflammatory mediators and causes neuroinflammation. The present study aimed to evaluate whether the ethanol-induced up-regulation of cytokines and chemokines is associated with anxiety-related behavior, 24 h after ethanol removal, and if TLR4 or TLR2 is involved in these effects. We used WT, TLR4-KO and TLR2-KO mice treated with alcohol for 5 months to show that chronic ethanol consumption increases the levels of cytokines (IL-1β, IL-17, TNF-α) and chemokines (MCP-1, MIP-1α, CX3CL1) in the striatum and serum (MCP-1, MIP-1α, CX3CL1) of WT mice. Alcohol deprivation for 24 h induces IFN-γ levels in the striatum and maintains high levels of some cytokines (IL-1β, IL-17) and chemokines (MIP-1α, CX3CL1) in this brain region. The latter events were associated with an increase in anxiogenic-related behavior, as evaluated by the dark and light box and the elevated plus maze tests. Notably, mice lacking TLR4 or TLR2 receptors are largely protected against ethanol-induced cytokine and chemokine release, and behavioral associated effects during alcohol abstinence. These data support the role of TLR4 and TLR2 responses in neuroinflammation and in anxiogenic-related behavior effects during ethanol deprivation, and also provide evidence that chemokines and cytokines can be biomarkers of ethanol-induced neuroimmune response.
•Ethanol treatment increases cytokine and chemokine levels in brain and serum.•Ethanol-deprivation changes brain cytokine levels and induces anxiety behavior.•The results highlight the role of neuroimmune/TLRs activation in cytokine production and anxiogenic-like effects in withdrawal.
Microglia are essential for CNS homeostasis and innate neuroimmune function, and play important roles in neurodegeneration and brain aging. Here we present gene expression profiles of purified ...microglia isolated at autopsy from the parietal cortex of 39 human subjects with intact cognition. Overall, genes expressed by human microglia were similar to those in mouse, including established microglial genes CX3CR1, P2RY12 and ITGAM (CD11B). However, a number of immune genes, not identified as part of the mouse microglial signature, were abundantly expressed in human microglia, including TLR, Fcγ and SIGLEC receptors, as well as TAL1 and IFI16, regulators of proliferation and cell cycle. Age-associated changes in human microglia were enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression and actin (dis)assembly. Limited overlap was observed in microglial genes regulated during aging between mice and humans, indicating that human and mouse microglia age differently.
The purpose of this study was to evaluate the impact of Chlorella vulgaris (5% in the diet), supplemented or not with two exogenous carbohydrase mixtures on piglets' performance, nutrient ...digestibility and gut morphology, fermentation products and microbiota. Forty-four male piglets weaned at 28 days of age, with 11.2 ± 0.46 kg of live weight, were used and assigned to 1 of 4 dietary treatments: cereal and soybean meal based-diet (control, n = 11), control diet with 5% of C. vulgaris (CH, n = 10), CH diet supplemented with 0.005% of Rovabio
Excel AP (CH + R, n = 10) and CH diet supplemented with 0.01% of a recombinant 4-carbohydrase mixture (CH + M, n = 11). Growth performance was not changed by the of C. vulgaris inclusion during 21 days of trial. However, total tract apparent digestibility of nutritional fractions was negatively impacted by the inclusion. In addition, the viscosity of duodenum plus jejunum contents slightly increased in all groups fed with the microalga. In contrast, dietary microalga increased duodenum villus height and promoted a healthier gut microbiota, with higher abundance of some specific bacterial taxa (Colidextribacter, Oscillospira and Lactobacillus). This study indicates that the dietary inclusion of 5% C. vulgaris improves piglets' gut health without impairing performance. Data also indicate that C. vulgaris reduces nutrient digestibility but promotes compensatory developments of gut mucosa and prebiotic effects. Dietary supplementation with exogenous carbohydrases does not seem to be necessary for this inclusion level. Therefore, the incorporation of CH as a sustainable feed ingredient in piglets' nutrition is a viable alternative approach.
In the present study, 199 pre-selected Carbohydrate-Active enZymes (CAZymes) and sulfatases were assessed, either alone or in combination, to evaluate their capacity to disrupt Laminaria digitata ...cell wall, with the consequent release of interesting nutritional compounds. A previously characterized individual alginate lyase, belonging to the family 7 of polysaccharide lyases (PL7) and produced by Saccharophagus degradans, was shown to be the most efficient in the in vitro degradation of L. digitata cell wall. The alginate lyase treatment, compared to the control, released up to 7.11 g/L of reducing sugars (p < 0.001) and 8.59 mmol/100 g dried alga of monosaccharides (p < 0.001), and reduced cell wall fluorescence intensity by 39.1% after staining with Calcofluor White (p = 0.001). The hydrolysis of gel-forming polymer alginate by the alginate lyase treatment could prevent the trapping of fatty acids and release beneficial monounsaturated fatty acids, particularly 18:1c9 (p < 0.001), to the extracellular medium. However, no liberation of proteins (p > 0.170) or pigments (p > 0.070) was observed. Overall, these results show the ability of an individual alginate lyase, from PL7 family, to partially degrade L. digitata cell wall under physiological conditions. Therefore, this CAZyme can potentially improve the bioavailability of L. digitata bioactive compounds for monogastric diets, with further application in feed industry.
In this study, a rational combination of 200 pre-selected Carbohydrate-Active enzymes (CAZymes) and sulfatases were tested, individually or combined, according to their ability to degrade Chlorella ...vulgaris cell wall to access its valuable nutritional compounds. The disruption of microalgae cell walls by a four-enzyme mixture (Mix) in comparison with the control, enabled to release up to 1.21 g/L of reducing sugars (p < 0.001), led to an eight-fold increase in oligosaccharides release (p < 0.001), and reduced the fluorescence intensity by 47% after staining with Calcofluor White (p < 0.001). The Mix treatment was successful in releasing proteins (p < 0.001), some MUFA (p < 0.05), and the beneficial 18:3n-3 fatty acid (p < 0.05). Even if no variation was detected for chlorophylls (p > 0.05), total carotenoids were increased in the supernatant (p < 0.05) from the Mix treatment, relative to the control. Taken together, these results indicate that this four-enzyme Mix displays an effective capacity to degrade C. vulgaris cell wall. Thus, these enzymes may constitute a good approach to improve the bioavailability of C. vulgaris nutrients for monogastric diets, in particular, and to facilitate the cost-effective use of microalgae by the feed industry, in general.
Roadmap on multiscale materials modeling van der Giessen, Erik; Schultz, Peter A; Bertin, Nicolas ...
Modelling and simulation in materials science and engineering,
06/2020, Letnik:
28, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that ...govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware.
► We review the population structure of Trypanosoma cruzi, causative agent of Chagas disease. ► We provide information on the eco-epidemiology of T. cruzi discrete typing units (DTUs). ► We outline ...the correlation of DTU with clinical manifestations. ► We summarize methods for DTU genotyping. ► Understanding of T. cruzi genetic diversity will provide new insights to future interventions.
The protozoan Trypanosoma cruzi, its mammalian reservoirs, and vectors have existed in nature for millions of years. The human infection, named Chagas disease, is a major public health problem for Latin America. T. cruzi is genetically highly diverse and the understanding of the population structure of this parasite is critical because of the links to transmission cycles and disease. At present, T. cruzi is partitioned into six discrete typing units (DTUs), TcI–TcVI. Here we focus on the current status of taxonomy-related areas such as population structure, phylogeographical and eco-epidemiological features, and the correlation of DTU with natural and experimental infection. We also summarize methods for DTU genotyping, available for widespread use in endemic areas. For the immediate future multilocus sequence typing is likely to be the gold standard for population studies. We conclude that greater advances in our knowledge on pathogenic and epidemiological features of these parasites are expected in the coming decade through the comparative analysis of the genomes from isolates of various DTUs.
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