SARSMutOnto: An Ontology for SARS-CoV-2 Lineages and Mutations

Artículo Materias > Biomedicina Universidad Europea del Atlántico > Investigación > Producción Científica
Fundación Universitaria Internacional de Colombia > Investigación > Producción Científica
Universidad Internacional Iberoamericana México > Investigación > Producción Científica
Universidad Internacional Iberoamericana Puerto Rico > Investigación > Producción Científica
Universidad Internacional do Cuanza > Investigación > Artículos y libros
Abierto Inglés Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in March 2020 is caused by the SARS-CoV-2 virus. The non-stop adaptive mutations of this virus and the emergence of several variants over time with characteristics favoring their spread constitute one of the biggest obstacles that researchers face in controlling this pandemic. Understanding the mutation mechanism allows for the adoption of anticipatory measures and the proposal of strategies to control its propagation. In this study, we focus on the mutations of this virus, and we propose the SARSMutOnto ontology to model SARS-CoV-2 mutations reported by Pango researchers. A detailed description is given for each mutation. The genes where the mutations occur and the genomic structure of this virus are also included. The sub-lineages and the recombinant sub-lineages resulting from these mutations are additionally represented while maintaining their hierarchy. We developed a Python-based tool to automatically generate this ontology from various published Pango source files. At the end of this paper, we provide some examples of SPARQL queries that can be used to exploit this ontology. SARSMutOnto might become a ‘wet bench’ machine learning tool for predicting likely future mutations based on previous mutations. metadata Bakkas, Jamal; Hanine, Mohamed; Chekry, Abderrahman; Gounane, Said; de la Torre Díez, Isabel; Lipari, Vivian; Martínez López, Nohora Milena y Ashraf, Imran mail SIN ESPECIFICAR, SIN ESPECIFICAR, SIN ESPECIFICAR, SIN ESPECIFICAR, SIN ESPECIFICAR, vivian.lipari@uneatlantico.es, nohora.martinez@uneatlantico.es, SIN ESPECIFICAR (2023) SARSMutOnto: An Ontology for SARS-CoV-2 Lineages and Mutations. Viruses, 15 (2). p. 505. ISSN 1999-4915

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Resumen

Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in March 2020 is caused by the SARS-CoV-2 virus. The non-stop adaptive mutations of this virus and the emergence of several variants over time with characteristics favoring their spread constitute one of the biggest obstacles that researchers face in controlling this pandemic. Understanding the mutation mechanism allows for the adoption of anticipatory measures and the proposal of strategies to control its propagation. In this study, we focus on the mutations of this virus, and we propose the SARSMutOnto ontology to model SARS-CoV-2 mutations reported by Pango researchers. A detailed description is given for each mutation. The genes where the mutations occur and the genomic structure of this virus are also included. The sub-lineages and the recombinant sub-lineages resulting from these mutations are additionally represented while maintaining their hierarchy. We developed a Python-based tool to automatically generate this ontology from various published Pango source files. At the end of this paper, we provide some examples of SPARQL queries that can be used to exploit this ontology. SARSMutOnto might become a ‘wet bench’ machine learning tool for predicting likely future mutations based on previous mutations.

Tipo de Documento: Artículo
Palabras Clave: ontology; genome structure; SARS-CoV-2; mutation; lineage
Clasificación temática: Materias > Biomedicina
Divisiones: Universidad Europea del Atlántico > Investigación > Producción Científica
Fundación Universitaria Internacional de Colombia > Investigación > Producción Científica
Universidad Internacional Iberoamericana México > Investigación > Producción Científica
Universidad Internacional Iberoamericana Puerto Rico > Investigación > Producción Científica
Universidad Internacional do Cuanza > Investigación > Artículos y libros
Depositado: 01 Mar 2023 23:30
Ultima Modificación: 21 Oct 2024 23:30
URI: https://repositorio.unic.co.ao/id/eprint/6097

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Mediterranean Diet and Quality of Life in Adults: A Systematic Review

Background/Objectives: With the increasing life expectancy and, as a result, the aging of the global population, there has been a rise in the prevalence of chronic conditions, which can significantly impact individuals’ health-related quality of life, a multidimensional concept that comprises an individual’s physical, mental, and social wellbeing. While a balanced, nutrient-dense diet, such as Mediterranean diet, is widely recognized for its role in chronic disease prevention, particularly in reducing the risk of cardiovascular diseases and certain cancers, its potential benefits extend beyond these well-known effects, showing promise in improving physical and mental wellbeing, and promoting health-related quality of life. Methods: A systematic search of the scientific literature in electronic databases (Pubmed/Medline) was performed to identify potentially eligible studies reporting on the relation between adherence to the Mediterranean diet and health-related quality of life, published up to December 2024. Results: A total of 28 studies were included in this systematic review, comprising 13 studies conducted among the general population and 15 studies involving various types of patients. Overall, most studies showed a significant association between adherence to the Mediterranean diet and HRQoL, with the most significant results retrieved for physical domains of quality of life, suggesting that diet seems to play a relevant role in both the general population and people affected by chronic conditions with an inflammatory basis. Conclusions: Adherence to the Mediterranean diet provides significant benefits in preventing and managing various chronic diseases commonly associated with aging populations. Furthermore, it enhances the overall health and quality of life of aging individuals, ultimately supporting more effective and less invasive treatment approaches for chronic diseases.

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Justyna Godos mail , Monica Guglielmetti mail , Cinzia Ferraris mail , Evelyn Frias-Toral mail , Irma Dominguez Azpíroz mail irma.dominguez@unini.edu.mx, Vivian Lipari mail vivian.lipari@uneatlantico.es, Andrea Di Mauro mail , Fabrizio Furnari mail , Sabrina Castellano mail , Fabio Galvano mail , Licia Iacoviello mail , Marialaura Bonaccio mail , Giuseppe Grosso mail ,

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Novel Transfer Learning Approach for Detecting Infected and Healthy Maize Crop Using Leaf Images

Maize is a staple crop worldwide, essential for food security, livestock feed, and industrial uses. Its health directly impacts agricultural productivity and economic stability. Effective detection of maize crop health is crucial for preventing disease spread and ensuring high yields. This study presents VG-GNBNet, an innovative transfer learning model that accurately detects healthy and infected maize crops through a two-step feature extraction process. The proposed model begins by leveraging the visual geometry group (VGG-16) network to extract initial pixel-based spatial features from the crop images. These features are then further refined using the Gaussian Naive Bayes (GNB) model and feature decomposition-based matrix factorization mechanism, which generates more informative features for classification purposes. This study incorporates machine learning models to ensure a comprehensive evaluation. By comparing VG-GNBNet's performance against these models, we validate its robustness and accuracy. Integrating deep learning and machine learning techniques allows VG-GNBNet to capitalize on the strengths of both approaches, leading to superior performance. Extensive experiments demonstrate that the proposed VG-GNBNet+GNB model significantly outperforms other models, achieving an impressive accuracy score of 99.85%. This high accuracy highlights the model's potential for practical application in the agricultural sector, where the precise detection of crop health is crucial for effective disease management and yield optimization.

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Novel transfer learning based bone fracture detection using radiographic images

A bone fracture is a medical condition characterized by a partial or complete break in the continuity of the bone. Fractures are primarily caused by injuries and accidents, affecting millions of people worldwide. The healing process for a fracture can take anywhere from one month to one year, leading to significant economic and psychological challenges for patients. The detection of bone fractures is crucial, and radiographic images are often relied on for accurate assessment. An efficient neural network method is essential for the early detection and timely treatment of fractures. In this study, we propose a novel transfer learning-based approach called MobLG-Net for feature engineering purposes. Initially, the spatial features are extracted from bone X-ray images using a transfer model, MobileNet, and then input into a tree-based light gradient boosting machine (LGBM) model for the generation of class probability features. Several machine learning (ML) techniques are applied to the subsets of newly generated transfer features to compare the results. K-nearest neighbor (KNN), LGBM, logistic regression (LR), and random forest (RF) are implemented using the novel features with optimized hyperparameters. The LGBM and LR models trained on proposed MobLG-Net (MobileNet-LGBM) based features outperformed others, achieving an accuracy of 99% in predicting bone fractures. A cross-validation mechanism is used to evaluate the performance of each model. The proposed study can improve the detection of bone fractures using X-ray images.

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Aneeza Alam mail , Ahmad Sami Al-Shamayleh mail , Nisrean Thalji mail , Ali Raza mail , Edgar Aníbal Morales Barajas mail , Ernesto Bautista Thompson mail ernesto.bautista@unini.edu.mx, Isabel de la Torre Diez mail , Imran Ashraf mail ,

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Hybrid Model with Wavelet Decomposition and EfficientNet for Accurate Skin Cancer Classification

Faced with anomalies in medical images, Deep learning is facing major challenges in detecting, diagnosing, and classifying the various pathologies that can be treated via medical imaging. The main challenges encountered are mainly due to the imbalance and variability of the data, as well as its complexity. The detection and classification of skin diseases is one such challenge that researchers are trying to overcome, as these anomalies present great variability in terms of appearance, texture, color, and localization, which sometimes makes them difficult to identify accurately and quickly, particularly by doctors, or by the various Deep Learning techniques on offer. In this study, an innovative and robust hybrid architecture is unveiled, underscoring the symbiotic potential of wavelet decomposition in conjunction with EfficientNet models. This approach integrates wavelet transformations with an EfficientNet backbone and incorporates advanced data augmentation, loss function, and optimization strategies. The model tested on the publicly accessible HAM10000 and ISIC2017 datasets has achieved an accuracy rate of 94.7%, and 92.2% respectively.

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Nut Consumption Is Associated with Cognitive Status in Southern Italian Adults

Background: Nut consumption has been considered a potential protective factor against cognitive decline. The aim of this study was to test whether higher total and specific nut intake was associated with better cognitive status in a sample of older Italian adults. Methods: A cross-sectional analysis on 883 older adults (>50 y) was conducted. A 110-item food frequency questionnaire was used to collect information on the consumption of various types of nuts. The Short Portable Mental Status Questionnaire was used to assess cognitive status. Multivariate logistic regression analyses were performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between nut intake and cognitive status after adjusting for potential confounding factors. Results: The median intake of total nuts was 11.7 g/day and served as a cut-off to categorize low and high consumers (mean intake 4.3 g/day vs. 39.7 g/day, respectively). Higher total nut intake was significantly associated with a lower prevalence of impaired cognitive status among older individuals (OR = 0.35, CI 95%: 0.15, 0.84) after adjusting for potential confounding factors. Notably, this association remained significant after additional adjustment for adherence to the Mediterranean dietary pattern as an indicator of diet quality, (OR = 0.32, CI 95%: 0.13, 0.77). No significant associations were found between cognitive status and specific types of nuts. Conclusions: Habitual nut intake is associated with better cognitive status in older adults.

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Justyna Godos mail , Francesca Giampieri mail francesca.giampieri@uneatlantico.es, Evelyn Frias-Toral mail , Raynier Zambrano-Villacres mail , Angel Olider Rojas Vistorte mail angel.rojas@uneatlantico.es, Vanessa Yélamos Torres mail vanessa.yelamos@funiber.org, Maurizio Battino mail maurizio.battino@uneatlantico.es, Fabio Galvano mail , Sabrina Castellano mail , Giuseppe Grosso mail ,

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