-
Clinical Immunology (Orlando, Fla.) Jun 2024Septic cardiomyopathy (SCM) is characterized by an abnormal inflammatory response and increased mortality. The role of efferocytosis in SCM is not well understood. We...
Integrated multi-omics analysis and machine learning developed diagnostic markers and prognostic model based on Efferocytosis-associated signatures for septic cardiomyopathy.
Septic cardiomyopathy (SCM) is characterized by an abnormal inflammatory response and increased mortality. The role of efferocytosis in SCM is not well understood. We used integrated multi-omics analysis to explore the clinical and genetic roles of efferocytosis in SCM. We identified six module genes (ATP11C, CD36, CEBPB, MAPK3, MAPKAPK2, PECAM1) strongly associated with SCM, leading to an accurate predictive model. Subgroups defined by EFFscore exhibited distinct clinical features and immune infiltration levels. Survival analysis showed that the C1 subtype with a lower EFFscore had better survival outcomes. scRNA-seq analysis of peripheral blood mononuclear cells (PBMCs) from sepsis patients identified four genes (CEBPB, CD36, PECAM1, MAPKAPK2) associated with high EFFscores, highlighting their role in SCM. Molecular docking confirmed interactions between diagnostic genes and tamibarotene. Experimental validation supported our computational results. In conclusion, our study identifies a novel efferocytosis-related SCM subtype and diagnostic biomarkers, offering new insights for clinical diagnosis and therapy.
PubMed: 38944364
DOI: 10.1016/j.clim.2024.110301 -
Chemosphere Jun 2024Predicting the parameters that influence colloidal phosphorus (CP) release from soils under different land uses is critical for managing the impact on water quality....
Predicting the parameters that influence colloidal phosphorus (CP) release from soils under different land uses is critical for managing the impact on water quality. Traditional modeling approaches, such as linear regression, may fail to represent the intricate relationships that exist between soil qualities and environmental influences. Therefore, in this study, we investigated the major determinants of CP release from different land use/types such as farmland, desert, forest soils, and rivers. The study utilizes the structural equation model (SEM), multiple linear regression (MLR), and three machine learning (ML) models (Random Forest (RF), Support Vector Regression (SVR), and eXtreme Gradient Boosting (XGBoost)) to predict the release of CP from different soils by using soil iron (Fe), aluminum (Al), calcium (Ca), pH, total organic carbon (TOC) and precipitation as independent variables. Results show that colloidal-cations (Fe, Al, Ca) and colloidal-TOC strongly influence CP release, while bioclimatic variables (precipitation) and pH have weaker effects. XGBoost outperforms the other models with an R of 0.94 and RMSE of 0.09. SHapley Additive Explanations described the outcomes since XGBoost is accurate. The relative relevance ranking indicated that colloidal TOC had the highest ranking in predicting CP. This was supported by the analysis of partial dependence plots, which showed that an increase in colloidal TOC increased soil CP release. According to our research, the SHAP XGBoost model provides significant information that can help determine the variables that considerably influence CP contents as compared to RF, SVM, and MLR.
PubMed: 38944354
DOI: 10.1016/j.chemosphere.2024.142699 -
Biotechnology Advances Jun 2024Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent... (Review)
Review
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment.
PubMed: 38944218
DOI: 10.1016/j.biotechadv.2024.108400 -
Methods (San Diego, Calif.) Jun 2024Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs...
Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs are synthesized as precursors or propeptides that undergo self-cleavage through autoproteolytic reaction. At present, APLs are grouped into 10 families belonging to six different clans of proteases. Recognizing their critical roles in many biological processes including virus maturation, and virulence, accurate identification and characterization of APLs is indispensable. Experimental identification and characterization of APLs is laborious and time-consuming. Here, we developed APLpred, a novel support vector machine (SVM) based predictor that can predict APLs from the primary sequences. APLpred was developed using Boruta-based optimal features derived from seven encodings and subsequently trained using five machine learning algorithms. After evaluating each model on an independent dataset, we selected APLpred (an SVM-based model) due to its consistent performance during cross-validation and independent evaluation. We anticipate APLpred will be an effective tool for identifying APLs. This could aid in designing inhibitors against these enzymes and exploring their functions. The APLpred web server is freely available at https://procarb.org/APLpred/.
PubMed: 38944134
DOI: 10.1016/j.ymeth.2024.05.014 -
Cell Reports. Medicine Jun 2024Infrared spectroscopy is a powerful technique for probing the molecular profiles of complex biofluids, offering a promising avenue for high-throughput in vitro...
Infrared spectroscopy is a powerful technique for probing the molecular profiles of complex biofluids, offering a promising avenue for high-throughput in vitro diagnostics. While several studies showcased its potential in detecting health conditions, a large-scale analysis of a naturally heterogeneous potential patient population has not been attempted. Using a population-based cohort, here we analyze 5,184 blood plasma samples from 3,169 individuals using Fourier transform infrared (FTIR) spectroscopy. Applying a multi-task classification to distinguish between dyslipidemia, hypertension, prediabetes, type 2 diabetes, and healthy states, we find that the approach can accurately single out healthy individuals and characterize chronic multimorbid states. We further identify the capacity to forecast the development of metabolic syndrome years in advance of onset. Dataset-independent testing confirms the robustness of infrared signatures against variations in sample handling, storage time, and measurement regimes. This study provides the framework that establishes infrared molecular fingerprinting as an efficient modality for populational health diagnostics.
PubMed: 38944038
DOI: 10.1016/j.xcrm.2024.101625 -
Biomedicine & Pharmacotherapy =... Jun 2024The integration of biochips with AI opened up new possibilities and is expected to revolutionize smart healthcare tools within the next five years. The combination of... (Review)
Review
The integration of biochips with AI opened up new possibilities and is expected to revolutionize smart healthcare tools within the next five years. The combination of miniaturized, multi-functional, rapid, high-throughput sample processing and sensing capabilities of biochips, with the computational data processing and predictive power of AI, allows medical professionals to collect and analyze vast amounts of data quickly and efficiently, leading to more accurate and timely diagnoses and prognostic evaluations. Biochips, as smart healthcare devices, offer continuous monitoring of patient symptoms. Integrated virtual assistants have the potential to send predictive feedback to users and healthcare practitioners, paving the way for personalized and predictive medicine. This review explores the current state-of-the-art biochip technologies including gene-chips, organ-on-a-chips, and neural implants, and the diagnostic and therapeutic utility of AI-assisted biochips in medical practices such as cancer, diabetes, infectious diseases, and neurological disorders. Choosing the appropriate AI model for a specific biomedical application, and possible solutions to the current challenges are explored. Surveying advances in machine learning models for biochip functionality, this paper offers a review of biochips for the future of biomedicine, an essential guide for keeping up with trends in healthcare, while inspiring cross-disciplinary collaboration among biomedical engineering, medicine, and machine learning fields.
PubMed: 38943990
DOI: 10.1016/j.biopha.2024.116997 -
Computers in Biology and Medicine Jun 2024The sit-to-stand (STS) movement is fundamental in daily activities, involving coordinated motion of the lower extremities and trunk, which leads to the generation of...
The sit-to-stand (STS) movement is fundamental in daily activities, involving coordinated motion of the lower extremities and trunk, which leads to the generation of joint moments based on joint angles and limb properties. Traditional methods for determining joint moments often involve sensors or complex mathematical approaches, posing limitations in terms of movement restrictions or expertise requirements. Machine learning (ML) algorithms have emerged as promising tools for joint moment estimation, but the challenge lies in efficiently selecting relevant features from diverse datasets, especially in clinical research settings. This study aims to address this challenge by leveraging metaheuristic optimization algorithms to predict joint moments during STS using minimal input data. Motion analysis data from 20 participants with varied mass and inertia properties are utilized, and joint angles are computed alongside simulations of joint moments. Feature selection is performed using the Manta Ray Foraging Optimization (MRFO), Marine Predators Algorithm (MPA), and Equilibrium Optimizer (EO) algorithms. Subsequently, Decision Tree Regression (DTR), Random Forest Regression (RFR), Extra Tree Regression (ETR), and eXtreme Gradient Boosting Regression (XGBoost Regression) ML algorithms are deployed for joint moment prediction. The results reveal EO-ETR as the most effective algorithm for ankle, knee, and neck joint moment prediction, while MPA-ETR exhibits superior performance for hip joint prediction. This approach demonstrates potential for enhancing accuracy in joint moment estimation with minimal feature input, offering implications for biomechanical research and clinical applications.
PubMed: 38943945
DOI: 10.1016/j.compbiomed.2024.108812 -
Journal of Hazardous Materials Jun 2024Biochar is effective in mitigating heavy metal pollution, and cadmium (Cd) is the primary pollutant in agricultural fields. However, traditional trial-and-error methods...
Biochar is effective in mitigating heavy metal pollution, and cadmium (Cd) is the primary pollutant in agricultural fields. However, traditional trial-and-error methods for determining the optimal biochar remediation efficiency are time-consuming and inefficient because of the varied soil, biochar, and Cd pollution conditions. This study employed the machine learning method to predict the Cd immobilization efficiency of biochar in soil. The predictive accuracy of the random forest (RF) model was superior to that of the other common linear and nonlinear models. Furthermore, to improve the reliability and accuracy of the RF model, it was optimized by employing a root-mean-squared-error-based trial-and-error approach. With the aid of the optimized model, the empirical categories for soil Cd immobilization efficiency were biochar properties (60.96 %) > experimental conditions (19.6 %) ≈ soil properties (19.44 %). Finally, this study identified the optimal biochar properties for enhancing agricultural soil Cd remediation in different regions of China, which was beneficial for decision-making regarding nationwide agricultural soil remediation using biochar. The immobilization effect of alkaline biochar was pronounced in acidic soils with relatively high organic matter. This study provides insights into the immobilization mechanism and an approach for biochar selection for Cd immobilization in agricultural soil.
PubMed: 38943890
DOI: 10.1016/j.jhazmat.2024.135065 -
Biosensors & Bioelectronics Jun 2024The progression of gastric cancer involves a complex multi-stage process, with gastroscopy and biopsy being the standard procedures for diagnosing gastric diseases. This...
Identification of chronic non-atrophic gastritis and intestinal metaplasia stages in the Correa's cascade through machine learning analyses of SERS spectral signature of non-invasively-collected human gastric fluid samples.
The progression of gastric cancer involves a complex multi-stage process, with gastroscopy and biopsy being the standard procedures for diagnosing gastric diseases. This study introduces an innovative non-invasive approach to differentiate gastric disease stage using gastric fluid samples through machine-learning-assisted surface-enhanced Raman spectroscopy (SERS). This method effectively identifies different stages of gastric lesions. The XGBoost algorithm demonstrates the highest accuracy of 96.88% and 91.67%, respectively, in distinguishing chronic non-atrophic gastritis from intestinal metaplasia and different subtypes of gastritis (mild, moderate, and severe). Through blinded testing validation, the model can achieve more than 80% accuracy. These findings offer new possibilities for rapid, cost-effective, and minimally invasive diagnosis of gastric diseases.
PubMed: 38943854
DOI: 10.1016/j.bios.2024.116530 -
Developmental Cognitive Neuroscience Jun 2024Heavy alcohol drinking is a major, preventable problem that adversely impacts the physical and mental health of US young adults. Studies seeking drinking risk factors...
Heavy alcohol drinking is a major, preventable problem that adversely impacts the physical and mental health of US young adults. Studies seeking drinking risk factors typically focus on young adults who enrolled in 4-year residential college programs (4YCP) even though most high school graduates join the workforce, military, or community colleges. We examined 106 of these understudied young adults (USYA) and 453 4YCPs from the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA) by longitudinally following their drinking patterns for 8 years from adolescence to young adulthood. All participants were no-to-low drinkers during high school. Whereas 4YCP individuals were more likely to initiate heavy drinking during college years, USYA participants did so later. Using mental health metrics recorded during high school, machine learning forecasted individual-level risk for initiating heavy drinking after leaving high school. The risk factors differed between demographically matched USYA and 4YCP individuals and between sexes. Predictors for USYA drinkers were sexual abuse, physical abuse for girls, and extraversion for boys, whereas 4YCP drinkers were predicted by the ability to recognize facial emotion and, for boys, greater openness. Thus, alcohol prevention programs need to give special consideration to those joining the workforce, military, or community colleges, who make up the majority of this age group.
PubMed: 38943839
DOI: 10.1016/j.dcn.2024.101413