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Classification and specific primer design for accurate detection of SARS-CoV-2 using deep learning.

In Scientific reports ; h5-index 158.0

In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from the National Genomics Data Center repository, separating the genome of different virus strains from the Coronavirus family with 98.73% accuracy. The network's behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from the National Center for Biotechnology Information and Global Initiative on Sharing All Influenza Data repositories, and are proven to be able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n = 6 previously tested positive), delivering a sensitivity similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both automatically identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics.

Lopez-Rincon Alejandro, Tonda Alberto, Mendoza-Maldonado Lucero, Mulders Daphne G J C, Molenkamp Richard, Perez-Romero Carmina A, Claassen Eric, Garssen Johan, Kraneveld Aletta D

2021-01-13

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Real-Time Implementation of EEG Oscillatory Phase-Informed Visual Stimulation Using a Least Mean Square-Based AR Model.

In Journal of personalized medicine

It is a technically challenging problem to assess the instantaneous brain state using electroencephalography (EEG) in a real-time closed-loop setup because the prediction of future signals is required to define the current state, such as the instantaneous phase and amplitude. To accomplish this in real-time, a conventional Yule-Walker (YW)-based autoregressive (AR) model has been used. However, the brain state-dependent real-time implementation of a closed-loop system employing an adaptive method has not yet been explored. Our primary purpose was to investigate whether time-series forward prediction using an adaptive least mean square (LMS)-based AR model would be implementable in a real-time closed-loop system or not. EEG state-dependent triggers synchronized with the EEG peaks and troughs of alpha oscillations in both an open-eyes resting state and a visual task. For the resting and visual conditions, statistical results showed that the proposed method succeeded in giving triggers at a specific phase of EEG oscillations for all participants. These individual results showed that the LMS-based AR model was successfully implemented in a real-time closed-loop system targeting specific phases of alpha oscillations and can be used as an adaptive alternative to the conventional and machine-learning approaches with a low computational load.

Shakeel Aqsa, Onojima Takayuki, Tanaka Toshihisa, Kitajo Keiichi

2021-Jan-11

Instantaneous phase, Yule–Walker (YW) method, alpha oscillation, autoregressive (AR) model, brain state-dependent stimulation, closed-loop, electroencephalography (EEG), least mean square (LMS) method

General General

Deep learning in the quest for compound nomination for fighting COVID-19.

In Current medicinal chemistry ; h5-index 49.0

The current COVID-19 pandemic gave rise to an unprecedented response from clinicians and the scientific community in all relevant biomedical fields. This created an incredible multidimensional data-rich framework in which deep learning proved instrumental to make sense of the data and build models used in prediction-validation workflows that in a matter of months have already produced results in assessing the spread of the outbreak, its taxonomy, population susceptibility, in diagnostics or drug discovery and repurposing. More is expected to come in the near future from using such advanced machine learning techniques in combating this pandemic. This review is aimed to uncover just a small fraction of this large global endeavor by focusing on the research performed on the main COVID-19 targets, on the computational weaponry used in identifying drugs to combat the disease, and on some of the most important directions found in confronting COVID-19 or alleviating its symptoms in the absence of vaccines or specific medication.

Mernea Maria, Martin Eliza C, Petrescu Andrei-José, Avram Speranta

2021-Jan-13

SARS-CoV-2, deep learning, drug design, drug repurposing.\n, drug-target interactions, virtual screening

General General

Age-group determination of living individuals using first molar images based on artificial intelligence.

In Scientific reports ; h5-index 158.0

Dental age estimation of living individuals is difficult and challenging, and there is no consensus method in adults with permanent dentition. Thus, we aimed to provide an accurate and robust artificial intelligence (AI)-based diagnostic system for age-group estimation by incorporating a convolutional neural network (CNN) using dental X-ray image patches of the first molars extracted via panoramic radiography. The data set consisted of four first molar images from the right and left sides of the maxilla and mandible of each of 1586 individuals across all age groups, which were extracted from their panoramic radiographs. The accuracy of the tooth-wise estimation was 89.05 to 90.27%. Performance accuracy was evaluated mainly using a majority voting system and area under curve (AUC) scores. The AUC scores ranged from 0.94 to 0.98 for all age groups, which indicates outstanding capacity. The learned features of CNNs were visualized as a heatmap, and revealed that CNNs focus on differentiated anatomical parameters, including tooth pulp, alveolar bone level, or interdental space, depending on the age and location of the tooth. With this, we provided a deeper understanding of the most informative regions distinguished by age groups. The prediction accuracy and heat map analyses support that this AI-based age-group determination model is plausible and useful.

Kim Seunghyeon, Lee Yeon-Hee, Noh Yung-Kyun, Park Frank C, Auh Q-Schick

2021-Jan-13

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Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract.

In Scientific reports ; h5-index 158.0

The gut microbiota's metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics' therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics' metabolic activity remains a formidable task. In order to solve this problem, an artificial model of the human gastrointestinal tract is introduced coined the ABIOME (A Bioreactor Imitation of the Microbiota Environment) and used to predict probiotic formulations' metabolic activity and hence therapeutic potential with machine learning tools. The ABIOME is a modular yet dynamic system with real-time monitoring of gastrointestinal conditions that support complex cultures representative of the human microbiota and its metabolome. The fecal-inoculated ABIOME was supplemented with a polyphenol-rich prebiotic and combinations of novel probiotics that altered the output of bioactive metabolites previously shown to invoke anti-inflammatory effects. To dissect the synergistic interactions between exogenous probiotics and the autochthonous microbiota a multivariate adaptive regression splines (MARS) model was implemented towards the development of optimized probiotic combinations with therapeutic benefits. Using this algorithm, several probiotic combinations were identified that stimulated synergistic production of bioavailable metabolites, each with a different therapeutic capacity. Based on these results, the ABIOME in combination with the MARS algorithm could be used to create probiotic formulations with specific therapeutic applications based on their signature metabolic activity.

Westfall Susan, Carracci Francesca, Estill Molly, Zhao Danyue, Wu Qing-Li, Shen Li, Simon James, Pasinetti Giulio Maria

2021-Jan-13

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Genetic diversity associated with natural rubber quality in elite genotypes of the rubber tree.

In Scientific reports ; h5-index 158.0

The objective of this study was to evaluate the genetic variability of natural rubber latex traits among 44 elite genotypes of the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell. Arg.]. Multivariate analysis and machine learning techniques were used, targeting the selection of parents that demonstrate superior characters. We analyzed traits related to technological or physicochemical properties of natural rubber latex, such as Wallace plasticity (P0), the plasticity retention index [PRI (%)], Mooney viscosity (VR), ash percentage (Ash), acetone extract percentage (AE), and nitrogen percentage (N), to study genetic diversity. Multivariate [unweighted pair group method with arithmetic means (UPGMA) and Tocher)] and machine learning techniques [K-means and Kohonen's self-organizing maps (SOMs)] were employed. The genotypes showed high genetic variability for some of the evaluated traits. The traits PRI, Ash, and PO contributed the most to genetic diversity. The genotypes were classified into six clusters by the UPGMA method, and the results were consistent with the Tocher, K-means and SOM results. PRI can be used to improve the industrial potential of clones. The clones IAC 418 and PB 326 were the most divergent, followed by IAC 404 and IAC 56. These genotypes and others from the IAC 500 and 400 series could be used to start a breeding program. These combinations offer greater heterotic potential than the others, which can be used to improve components of rubber latex quality. Thus, it is important to consider the quality of rubber latex in the early stage of breeding programs.

Sant’Anna Isabela de Castro, Gouvêa Ligia Regina Lima, Martins Maria Alice, Scaloppi Junior Erivaldo José, de Freitas Rogério Soares, Gonçalves Paulo de Souza

2021-Jan-13