AIMC Topic: Bacteria
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Virtual Gram staining of label-free bacteria using dark-field microscopy and deep learning.
Science advances
Jan 8, 2025
Gram staining has been a frequently used staining protocol in microbiology. It is vulnerable to staining artifacts due to, e.g., operator errors and chemical variations. Here, we introduce virtual Gram staining of label-free bacteria using a trained ...
Open-set deep learning-enabled single-cell Raman spectroscopy for rapid identification of airborne pathogens in real-world environments.
Science advances
Jan 8, 2025
Pathogenic bioaerosols are critical for outbreaks of airborne disease; however, rapidly and accurately identifying pathogens directly from complex air environments remains highly challenging. We present an advanced method that combines open-set deep ...
SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.
NAR genomics and bioinformatics
Jan 7, 2025
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokar...
Effects of data transformation and model selection on feature importance in microbiome classification data.
Microbiome
Jan 4, 2025
BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, composi...
Gut microbial composition associated with risk of premature aging in women with Yin-deficiency constitution.
Frontiers in cellular and infection microbiology
Jan 3, 2025
BACKGROUND: Yin-deficiency constitution (YinDC) refers to a traditional Chinese medicine concept, characterized by an imbalance state that includes an imbalance in the gut microbiota, resulting from a relative deficiency of Yin fluids within the body...
Machine Learning-Enhanced Bacteria Detection Using a Fluorescent Sensor Array with Functionalized Graphene Quantum Dots.
ACS applied materials & interfaces
Jan 2, 2025
Pathogenic bacteria are the source of many serious health problems, such as foodborne diseases and hospital infections. Timely and accurate detection of these pathogens is of vital significance for disease prevention, control of epidemic spread, and ...
DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.
Scientific reports
Dec 30, 2024
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Tradi...
Machine learning-based prediction of non-aeration linear alkylbenzene sulfonate mineralization in an oxygenic microalgal-bacteria biofilm.
Bioresource technology
Dec 28, 2024
Microalgal-bacteria biofilm shows great potential in low-cost greywater treatment. Accurately predicting treated greywater quality is of great significance for water reuse. In this work, machine learning models were developed for simulating and predi...
A calibration framework toward model generalization for bacteria concentration estimation in water resource recovery facilities.
Scientific reports
Dec 28, 2024
Reduced bacteria concentrations in wastewater is a key indicator of the efficacy of water resource recovery facilities (WRRFs). However, monitoring the presence of bacterial concentrations in real time at each stage of the WRRF is challenging as it r...
Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation.
Journal of hazardous materials
Dec 25, 2024
Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to ide...
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