Michihiro Araki
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View article: Metabolic and plasmid engineering to produce D-phenyllactic acid from glucose–xylose co-substrates in <i>Escherichia coli</i>
Metabolic and plasmid engineering to produce D-phenyllactic acid from glucose–xylose co-substrates in <i>Escherichia coli</i> Open
Plasmid DNA comprises various modules, including promoter and terminator regions, replication origins, and antibiotic resistance genes as selection markers. The 5′UTRs of the promoter and ribosome binding site (RBS) have been extensively s…
View article: Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions
Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions Open
Mass-based fingerprinting can characterize microorganisms; however, expansion of these methods to predict specific gene functions is lacking. Therefore, mass fingerprinting was developed to functionally profile a yeast knockout library. Ma…
View article: The Cost-Effectiveness of Increased Yogurt Intake in Type 2 Diabetes in Japan
The Cost-Effectiveness of Increased Yogurt Intake in Type 2 Diabetes in Japan Open
Background/Objectives: A healthy diet helps prevent noncommunicable diseases, and dairy is an essential part of this diet. Multiple meta-analyses have shown an inverse association between yogurt intake and type 2 diabetes (T2D). This study…
View article: Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis
Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis Open
In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energ…
View article: Large language models and questions from older adults: a human and machine-based evaluation study
Large language models and questions from older adults: a human and machine-based evaluation study Open
Large language models (LLMs) hold the potential to offer substantial advantages in information generation and comprehension. This study seeks to evaluate the extent to which these models can effectively meet the needs of older adults by ex…
View article: Disease Prediction Using Machine Learning on Smartphone-Based Eye, Skin, and Voice Data: Scoping Review
Disease Prediction Using Machine Learning on Smartphone-Based Eye, Skin, and Voice Data: Scoping Review Open
Background The application of machine learning methods to data generated by ubiquitous devices like smartphones presents an opportunity to enhance the quality of health care and diagnostics. Smartphones are ideal for gathering data easily,…
View article: Machine Learning Model for Predicting Coronary Heart Disease Risk: Development and Validation Using Insights From a Japanese Population–Based Study
Machine Learning Model for Predicting Coronary Heart Disease Risk: Development and Validation Using Insights From a Japanese Population–Based Study Open
Background Coronary heart disease (CHD) is a major cause of morbidity and mortality worldwide. Identifying key risk factors is essential for effective risk assessment and prevention. A data-driven approach using machine learning (ML) offer…
View article: Prediction of depressive disorder using machine learning approaches: findings from the NHANES
Prediction of depressive disorder using machine learning approaches: findings from the NHANES Open
We developed ML models to predict depression and utilized SHAP for interpretation. This approach identifies key factors associated with depression, encompassing socioeconomic, demographic, and health-related aspects.
View article: Correction: Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling
Correction: Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling Open
[This corrects the article DOI: 10.1371/journal.pone.0261654.].
View article: Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions
Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions Open
Mass-based fingerprinting can characterize unknown strains, however expansion of these methods to predict specific gene functions is lacking. Therefore, rapid mass fingerprinting was developed to functionally profile a comprehensive yeast …
View article: Machine Learning-Based Prediction of Coronary Heart Disease: Comprehensive Insights from the Suita Study (Preprint)
Machine Learning-Based Prediction of Coronary Heart Disease: Comprehensive Insights from the Suita Study (Preprint) Open
BACKGROUND Coronary heart disease (CHD) is a major cause of morbidity and mortality worldwide. Identifying key risk factors is essential for effective risk assessment and prevention. Machine learning (ML) offers advanced methods for analy…
View article: Machine Learning Approaches for Stroke Risk Prediction: Findings from the Suita Study
Machine Learning Approaches for Stroke Risk Prediction: Findings from the Suita Study Open
Stroke constitutes a significant public health concern due to its impact on mortality and morbidity. This study investigates the utility of machine learning algorithms in predicting stroke and identifying key risk factors using data from t…
View article: Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis
Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis Open
Background Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compound…
View article: Machine Learning Approaches for Stroke Risk Prediction: Findings from the Suita Study
Machine Learning Approaches for Stroke Risk Prediction: Findings from the Suita Study Open
Stroke constitutes a significant public health concern due to its impact on mortality and morbidity. This study investigates the utility of machine learning algorithms in predicting stroke and identifying key risk factors using data from t…
View article: Unveiling Coronary Heart Disease Prediction through Machine Learning Techniques: Insights from the Suita Population-Based Cohort Study
Unveiling Coronary Heart Disease Prediction through Machine Learning Techniques: Insights from the Suita Population-Based Cohort Study Open
We leveraged machine learning (ML) techniques, namely logistic regression (LR), random forest (RF), support vector machine (SVM), extreme gradient boosting (XGBoost), and LightGBM to predict coronary heart disease (CHD) and identify the ke…
View article: Development of a Machine Learning Model for Classifying Cooking Recipes According to Dietary Styles
Development of a Machine Learning Model for Classifying Cooking Recipes According to Dietary Styles Open
To complement classical methods for identifying Japanese, Chinese, and Western dietary styles, this study aimed to develop a machine learning model. This study utilized 604 features from 8183 cooking recipes based on a Japanese recipe site…
View article: Predicting Cardiovascular Disease Mortality: Leveraging Machine Learning for Comprehensive Assessment of Health and Nutrition Variables
Predicting Cardiovascular Disease Mortality: Leveraging Machine Learning for Comprehensive Assessment of Health and Nutrition Variables Open
Cardiovascular disease (CVD) is one of the primary causes of death around the world. This study aimed to identify risk factors associated with CVD mortality using data from the National Health and Nutrition Examination Survey (NHANES). We …
View article: Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study
Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study Open
A cross-sectional study involving 224 healthy Japanese adult females explored the relationship between ramen intake, gut microbiota diversity, and blood biochemistry. Using a stepwise regression model, ramen intake was inversely associated…
View article: Using Explainable AI to understand frailty indicators
Using Explainable AI to understand frailty indicators Open
Introduction The prevalence of frailty is on the rise with the aging population and increasing life expectancy, which often is accompanied by comorbidities. Frailty can be effectively detected using Frailty index such as KCL index. Early d…
View article: Different Recognition of Protein Features Depending on Deep Learning Models: A Case Study of Aromatic Decarboxylase UbiD
Different Recognition of Protein Features Depending on Deep Learning Models: A Case Study of Aromatic Decarboxylase UbiD Open
The number of unannotated protein sequences is explosively increasing due to genome sequence technology. A more comprehensive understanding of protein functions for protein annotation requires the discovery of new features that cannot be c…
View article: Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli
Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli Open
Omics data was acquired, and the development and research of metabolic simulation and analysis methods using them were also actively carried out. However, it was a laborious task to acquire such data each time the medium composition, cultu…
View article: Engineered enzymatically active bacteriophages and methods of uses thereof
Engineered enzymatically active bacteriophages and methods of uses thereof Open
The present invention provides engineered bacteriophages that express at least one biofilm degrading enzyme on their surface and uses thereof for degrading bacterial biofilms. The invention also provides genetically engineered bacteriophag…
View article: EnzymeNet: residual neural networks model for Enzyme Commission number prediction
EnzymeNet: residual neural networks model for Enzyme Commission number prediction Open
Motivation Enzymes are key targets to biosynthesize functional substances in metabolic engineering. Therefore, various machine learning models have been developed to predict Enzyme Commission (EC) numbers, one of the enzyme annotations. Ho…
View article: Predicting Overweight and Obesity Status Among Malaysian Working Adults With Machine Learning or Logistic Regression: Retrospective Comparison Study
Predicting Overweight and Obesity Status Among Malaysian Working Adults With Machine Learning or Logistic Regression: Retrospective Comparison Study Open
Background Overweight or obesity is a primary health concern that leads to a significant burden of noncommunicable disease and threatens national productivity and economic growth. Given the complexity of the etiology of overweight or obesi…
View article: Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling
Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling Open
Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in materi…
View article: Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling
Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling Open
Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in materi…