Biomarker selection and a prospective metabolite-based machine learning diagnostic for lyme disease

Apoptosis and NETotic cell death affect diabetic nephropathy independently: An study integrative study encompassing bioinformatics, machine learning, and experimental validation

OBJECTIVE

Although programmed cell death (PCD) and diabetic nephropathy (DN) are intrinsically conneted, the interplay among various PCD forms remains elusive. In this study, We aimed at identifying independently DN-associated PCD pathways and biomarkers relevant to the related pathogenesis.

METHODS

We acquired DN-related datasets from the GEO database and identified PCDs independently correlated with DN (DN-PCDs) through single-sample Gene Set Enrichment Analysis (ssGSEA) as well as, univariate and multivariate logistic regression analyses. Subsequently, applying differential expression analysis, weighted gene co-expression network analysis (WGCNA), and Mfuzz cluster analysis, we filtered the DN-PCDs pertinent to DN onset and progression. The convergence of various machine learning techniques ultimately spotlighted hub genes, substantiated through dataset meta-analyses and experimental validations, thereby confirming hub genes and related pathways expression consistencies.

RESULTS

We harmonized four DN-related datasets (GSE1009, GSE142025, GSE30528, and GSE30529) post-batch-effect removal for subsequent analyses. Our differential expression analysis yielded 709 differentially expressed genes (DEGs), comprising 446 upregulated and 263 downregulated DEGs. Based on our ssGSEA as well as univariate and multivariate logistic regressions, apoptosis and NETotic cell death were appraised as independent risk factors for DN (Odds Ratio > 1, p < 0.05). Next, we further refined 588 apoptosis- and NETotic cell death-associated genes through WGCNA and Mfuzz analysis, resulting in the identification of 17 DN-PCDs. Integrating protein-protein interaction (PPI) network analyses, network topology, and machine learning, we pinpointed hub genes (e.g., IL33, RPL11, and CX3CR1) as significant DN risk factors with expression corroborating in subsequent meta-analyses and experimental validations. Our GSEA enrichment analysis discerned differential enrichments between DN and control samples within pathways such as IL2/STAT5, IL6/JAK/STAT3, TNF-α via NF-κB, apoptosis, and oxidative phosphorylation, with related proteins such as IL2, IL6, and TNFα, which we subsequently submitted to experimental verification.

CONCLUSION

Innovatively stemming from from PCD interactions, in this study, we discerned PCDs with an independent impact on DN: apoptosis and NETotic cell death. We further screened DN evolution- and progression-related biomarkers, i.e. IL33, RPL11, and CX3CR1, all of which we empirically validated. This study not only poroposes a PCD-centric perspective for DN studies but also provides evidence for PCD-mediated immune cell infiltration exploration in DN regulation. Our results could motivate further exploration of DN pathogenesis, such as how the inflammatory microenvironment mediates NETotic cell death in DN regulation, representing a promising direction for future research.

Lyme rashes disease classification using deep feature fusion technique

Automatic classification of Lyme disease rashes on the skin helps clinicians and dermatologists' probe and investigate Lyme skin rashes effectively. This paper proposes a new in-depth features fusion system to classify Lyme disease rashes. The proposed method consists of two main steps. First, three different deep learning models, Densenet201, InceptionV3, and Exception, were trained independently to extract the deep features from the erythema migrans (EM) images. Second, a deep feature fusion mechanism (meta classifier) is developed to integrate the deep features before the final classification output layer. The meta classifier is a basic deep convolutional neural network trained on original images and features extracted from base level three deep learning models. In the feature fusion mechanism, the last three layers of base models are dropped out and connected to the meta classifier. The proposed deep feature fusion method significantly improved the classification process, where the classification accuracy was 98.97%, which is particularly impressive than the other state-of-the-art models.

Unleashing the power of artificial intelligence for diagnosing and treating infectious diseases: A comprehensive review

Infectious diseases present a global challenge, requiring accurate diagnosis, effective treatments, and preventive measures. Artificial intelligence (AI) has emerged as a promising tool for analysing complex molecular data and improving the diagnosis, treatment, and prevention of infectious diseases. Computer-aided detection (CAD) using convolutional neural networks (CNN) has gained prominence for diagnosing tuberculosis (TB) and other infectious diseases such as COVID-19, HIV, and viral pneumonia. The review discusses the challenges and limitations associated with AI in this field and explores various machine-learning models and AI-based approaches. Artificial neural networks (ANN), recurrent neural networks (RNN), support vector machines (SVM), multilayer neural networks (MLNN), CNN, long short-term memory (LSTM), and random forests (RF) are among the models discussed. The review emphasizes the potential of AI to enhance the accuracy and efficiency of diagnosis, treatment, and prevention of infectious diseases, highlighting the need for further research and development in this area.

Physics-informed neural entangled-ladder network for inhalation impedance of the respiratory system

BACKGROUND AND OBJECTIVES

The use of machine learning methods for modelling bio-systems is becoming prominent which can further improve bio-medical technologies. Physics-informed neural networks (PINNs) can embed the knowledge of physical laws that govern a system during the model training process. PINNs utilise differential equations in the model which traditionally used numerical methods that are computationally complex.

METHODS

We integrate PINNs with an entangled ladder network for modelling respiratory systems by considering a lungs conduction zone to evaluate the respiratory impedance for different initial conditions. We evaluate the respiratory impedance for the inhalation phase of breathing for a symmetric model of the human lungs using entanglement and continued fractions.

RESULTS

We obtain the impedance of the conduction zone of the lungs pulmonary airways using PINNs for nine different combinations of velocity and pressure of inhalation. We compare the results from PINNs with the finite element method using the mean absolute error and root mean square error. The results show that the impedance obtained with PINNs contrasts with the conventional forced oscillation test used for deducing the respiratory impedance. The results show similarity with the impedance plots for different respiratory diseases.

CONCLUSION

We find a decrease in impedance when the velocity of breathing is lowered gradually by 20%. Hence, the methodology can be used to design smart ventilators to the improve flow of breathing.

Using machine learning to determine the time of exposure to infection by a respiratory pathogen

Given an infected host, estimating the time that has elapsed since initial exposure to the pathogen is an important problem in public health. In this paper we use longitudinal gene expression data from human challenge studies of viral respiratory illnesses for building predictive models to estimate the time elapsed since onset of respiratory infection. We apply sparsity driven machine learning to this time-stamped gene expression data to model the time of exposure by a pathogen and subsequent infection accompanied by the onset of the host immune response. These predictive models exploit the fact that the host gene expression profile evolves in time and its characteristic temporal signature can be effectively modeled using a small number of features. Predicting the time of exposure to infection to be in first 48 h after exposure produces BSR in the range of 80-90% on sequestered test data. A variety of machine learning experiments provide evidence that models developed on one virus can be used to predict exposure time for other viruses, e.g., H1N1, H3N2, and HRV. The interferon [Formula: see text] signaling pathway appears to play a central role in keeping time from onset of infection. Successful prediction of the time of exposure to a pathogen has potential ramifications for patient treatment and contact tracing.

Wearable chemical sensors for biomarker discovery in the omics era

Biomarkers are crucial biological indicators in medical diagnostics and therapy. However, the process of biomarker discovery and validation is hindered by a lack of standardized protocols for analytical studies, storage and sample collection. Wearable chemical sensors provide a real-time, non-invasive alternative to typical laboratory blood analysis, and are an effective tool for exploring novel biomarkers in alternative body fluids, such as sweat, saliva, tears and interstitial fluid. These devices may enable remote at-home personalized health monitoring and substantially reduce the healthcare costs. This Review introduces criteria, strategies and technologies involved in biomarker discovery using wearable chemical sensors. Electrochemical and optical detection techniques are discussed, along with the materials and system-level considerations for wearable chemical sensors. Lastly, this Review describes how the large sets of temporal data collected by wearable sensors, coupled with modern data analysis approaches, would open the door for discovering new biomarkers towards precision medicine.

Precision Medicine Approaches with Metabolomics and Artificial Intelligence

Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and machine learning methods, which are fundamental to managing large number of variables and samples. In the present review, we reported and discussed the application of artificial intelligence (AI) strategies for metabolomics data analysis. Particularly, we focused on widely used non-linear machine learning classifiers, such as ANN, random forest, and support vector machine (SVM) algorithms. A discussion of recent studies and research focused on disease classification, biomarker identification and early diagnosis is presented. Challenges in the implementation of metabolomics–AI systems, limitations thereof and recent tools were also discussed.

Recent Advances in the Immunologic Method Applied to Tick-Borne Diseases in Brazil

Zoonotic-origin infectious diseases are one of the major concerns of human and veterinary health systems. Ticks, as vectors of several zoonotic diseases, are ranked second only to mosquitoes as vectors. Many ticks’ transmitted infections are still endemic in the Americas, Europe, and Africa and represent approximately 17% of their infectious diseases population. Although our scientific capacity to identify and diagnose diseases is increasing, it remains a challenge in the case of tick-borne conditions. For example, in 2017, 160 cases of the Brazilian Spotted Fever (BSF, a tick-borne illness) were confirmed, alarming the notifiable diseases information system. Conversely, Brazilian borreliosis and ehrlichiosis do not require notification. Still, an increasing number of cases in humans and dogs have been reported in southeast and northeastern Brazil. Immunological methods applied to human and dog tick-borne diseases (TBD) show low sensitivity and specificity, cross-reactions, and false IgM positivity. Thus, the diagnosis and management of TBD are hampered by the personal tools and indirect markers used. Therefore, specific and rapid methods urgently need to be developed to diagnose the various types of tick-borne bacterial diseases. This review presents a brief historical perspective on the evolution of serological assays and recent advances in diagnostic tests for TBD (ehrlichiosis, BSF, and borreliosis) in humans and dogs, mainly applied in Brazil. Additionally, this review covers the emerging technologies available in diagnosing TBD, including biosensors, and discusses their potential for future use as gold standards in diagnosing these diseases.