Classification and selection of the main features for the identification of toxicity in Agaricus and Lepiota with machine learning algorithms.

The occurrence of fungi is cosmopolitan, and while some mushroom species are beneficial to human health, others can be toxic and cause illness problems. This study aimed to analyze the organoleptic, ecological, and morphological characteristics of a group of fungal specimens and identify the most significant features to develop models for fungal toxicity classification using genetic algorithms and LASSO regression. The results of the study indicated that odor, spore print color, and habitat were the most significant characteristics identified by the genetic algorithm GALGO. Meanwhile, odor, gill size, stalk shape, and twelve other features were the relevant characteristics identified by LASSO regression. The importance score of the odor variable was 99.99%, gill size obtained 73.7%, stalk shape scored 39.9%, and the remaining variables did not score higher than 18%. Logistic regression, k-nearest neighbor (KNN), and XG-Boost classification algorithms were used to develop models using the features selected by both GALGO and LASSO. The models were evaluated using sensitivity, specificity, and accuracy metrics. The models with the highest AUC values were XGBoost, with a maximum value of 0.99 using the features selected by LASSO, followed by KNN with a maximum value of 0.99. The GALGO selection resulted in a maximum AUC of 0.98 in KNN and XGBoost. The models developed in this study have the potential to aid in the accurate identification of toxic fungi, which can prevent health problems caused by their consumption.

Comparative study of convolutional neural network architectures for gastrointestinal lesions classification.

The gastrointestinal (GI) tract can be affected by different diseases or lesions such as esophagitis, ulcers, hemorrhoids, and polyps, among others. Some of them can be precursors of cancer such as polyps. Endoscopy is the standard procedure for the detection of these lesions. The main drawback of this procedure is that the diagnosis depends on the expertise of the doctor. This means that some important findings may be missed. In recent years, this problem has been addressed by deep learning (DL) techniques. Endoscopic studies use digital images. The most widely used DL technique for image processing is the convolutional neural network (CNN) due to its high accuracy for modeling complex phenomena. There are different CNNs that are characterized by their architecture. In this article, four architectures are compared: AlexNet, DenseNet-201, Inception-v3, and ResNet-101. To determine which architecture best classifies GI tract lesions, a set of metrics; accuracy, precision, sensitivity, specificity, F1-score, and area under the curve (AUC) were used. These architectures were trained and tested on the HyperKvasir dataset. From this dataset, a total of 6,792 images corresponding to 10 findings were used. A transfer learning approach and a data augmentation technique were applied. The best performing architecture was DenseNet-201, whose results were: 97.11% of accuracy, 96.3% sensitivity, 99.67% specificity, and 95% AUC.

Demographic and Comorbidities Data Description of Population in Mexico with SARS-CoV-2 Infected Patients(COVID19): An Online Tool Analysis.

The Word Health Organization (WHO) declared in March 2020 that we are facing a pandemic designated as COVID-19, which is the acronym of coronavirus disease 2019, caused by a new virus know as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In Mexico, the first cases of COVID-19, was reported by the Secretary of Health on 28 February 2020. More than sixteen thousand cases and more than fifteen thousand deaths have been reported in Mexico, and it continues to rise; therefore, this article proposes two online visualization tools (a web platform) that allow the analysis of demographic data and comorbidities of the Mexican population. The objective of these tools is to provide graphic information, fast and updated, based on dataset obtained directly from National Governments Health Secretary (Secretaría de Salud, SSA) which is daily refreshed with the information related to SARS-CoV-2. To allow a dynamical update and friendly interface, and approach with R-project, a well-known Open Source language and environment for statistical computing and Shiny package, were implemented. The dataset is loaded automatically from the latest version released by the federal government of Mexico. Users can choose to study particular groups determined by gender, entity, type of result (positive, negative, pending outcome) and comorbidity. The image results are plots that can be instantly interpreted and supported by the text summary. This tool, in addition to being a consultation for the general public, is useful in Public Health to facilitate the visualization of the data, allowing its timely interpretation due to the changing nature of COVID-19, it can even be used for decision-making by leaders, for the benefit of the health of the community.

Deep artificial neural network based on environmental sound data for the generation of a children activity classification model.

Children activity recognition (CAR) is a subject for which numerous works have been developed in recent years, most of them focused on monitoring and safety. Commonly, these works use as data source different types of sensors that can interfere with the natural behavior of children, since these sensors are embedded in their clothes. This article proposes the use of environmental sound data for the creation of a children activity classification model, through the development of a deep artificial neural network (ANN). Initially, the ANN architecture is proposed, specifying its parameters and defining the necessary values for the creation of the classification model. The ANN is trained and tested in two ways: using a 70-30 approach (70% of the data for training and 30% for testing) and with a k-fold cross-validation approach. According to the results obtained in the two validation processes (70-30 splitting and k-fold cross validation), the ANN with the proposed architecture achieves an accuracy of 94.51% and 94.19%, respectively, which allows to conclude that the developed model using the ANN and its proposed architecture achieves significant accuracy in the children activity classification by analyzing environmental sound.

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer.

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures.

Nested case-control study reveals increased levels of urinary proteins from human kidney toxicity panels in women predicted to develop preeclampsia.

PURPOSE: The aim of this study was to evaluate the usefulness of urine concentrations of 12 proteins as a risk parameter for developing preeclampsia (PE). METHODS: A nested case-control study was designed to determine protein concentrations in urine from women predicted to develop PE (WPD-PE) and normotensive pregnancies (controls). Protein profiles were determined at 12, 16 and 20 gestational weeks (GW) using the Bio-Plex Pro human kidney toxicity Panel 1 and Panel 2 (Bio-Rad). Receiver operating characteristic (ROC) curve analyses were performed. Correlations between proteins and clinical parameters at the time of PE diagnosis were also assessed. RESULTS: Significant differences were observed in urine cystatin C (Cys C) levels at 16 and 20 GW and clusterin at 20 GW between WPD-PE and controls (P < 0.05). ROC analysis revealed that Cys C at 16 GW had the highest area under the ROC curve (0.758). At 16 GW, patients with urine Cys C levels above 73.7 ng/mL had eightfold increased odds for developing PE (odds ratio 7.92; 95 % CI 1.3-47.5; P = 0.027). A positive correlation was found between urinary Cys C (at 16 and 20 GW) and leukocyte counts, total proteins, aspartate aminotransferase, alanine aminotransferase, bilirubin and lactate dehydrogenase at the time of PE diagnosis (P value < 0.05). CONCLUSIONS: Urinary Cys C and clusterin showed predictive value for PE development in our cohort. Further studies are needed to validate their use as predictive biomarkers for PE and/or their participation in PE pathogenesis.