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Background: Genomic data is essential for clinical decision-making in precision oncology. Bioinformatic algorithms are widely used to analyze next-generation sequencing (NGS) data, but they face two major challenges. First, these pipelines are highly complex, involving multiple steps and the integration of various tools.
View Article and Find Full Text PDFConstruction of feature selection and efficacy prediction model for transformation therapy of locally advanced pancreatic cancer based on CT, F-FDG PET/CT, DNA mutation, and CA199.
Cancer Cell Int
January 2025
The Comprehensive Cancer Centre, Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, 321 Zhongshan Road, Nanjing, 210008, China.
Background: Immunotherapy and radiotherapy play crucial roles in the transformation therapy of locally advanced pancreatic cancer; however, the exploration of effective predictive biomarkers has been unsatisfactory. With the rapid development of radiomics, next-generation sequencing, and machine learning, there is hope to identify biomarkers that can predict the efficacy of transformative treatment for locally advanced pancreatic cancer through simple and non-invasive clinical methods. Our study focuses on using computed tomography (CT), positron emission tomography/computed tomography (PET/CT), gene mutations, and baseline carbohydrate antigen 199 (CA199) to identify biomarkers for predicting the efficacy of transformative treatment.
View Article and Find Full Text PDFNext-generation metabolic models informed by biomolecular simulations.
Curr Opin Biotechnol
January 2025
Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; Nanovaccine Institute, Iowa State University, Ames, IA, USA. Electronic address:
Metabolic modeling is essential for understanding the mechanistic bases of cellular metabolism in various organisms, from microbes to humans, and the design of fitter microbial strains. Metabolic networks focus on the overall fluxes through biochemical reactions that implicitly rely on several biochemical processes, such as active or diffusive uptake (or export) of nutrients (or metabolites), enzymatic turnover of metabolites, and metal-cofactor enzyme interactions. Despite independent progress in biomolecular simulations, they have yet to be integrated to inform metabolic models.
View Article and Find Full Text PDFGraph-based deep learning for predictions on changes in microbiomes and biogas production in anaerobic digestion systems.
Water Res
January 2025
School of Civil, Environmental, and Architectural Engineering, Korea University, Seoul 02841, Korea. Electronic address:
Anaerobic digestion (AD), which relies on a complex microbial consortium for efficient biogas generation, is a promising avenue for renewable energy production and organic waste treatment. However, understanding and optimising AD processes are challenging because of the intricate interactions within microbial communities and the impact of volatile fatty acids (VFAs) on biogas production. To address these challenges, this study proposes the application of graph convolutional networks (GCNs) to comprehensively model AD processes.
View Article and Find Full Text PDFMapping out strategies to further develop human-relevant, new approach methodology (NAM)-based developmental neurotoxicity (DNT) testing.
ALTEX
January 2025
In vitro toxicology and biomedicine, inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany.
On occasion of the DNT5 meeting in Konstanz, Germany (April-2024), participants brainstormed on future challenges concerning a regulatory implementation of the developmental neurotoxicity (DNT) in vitro test battery (DNT-IVB). The five discussion topics below outline some of the key issues, opportunities and research directions for the next several years: (1) How to contextualize DNT hazard with information on potential maternal toxicity or other toxicity domains (non-DNT)? Several approaches on how to use cytotoxicity data from NAMs were discussed. (2) What opportunities exist for an immediate or near-future application of the DNT-IVB, e.
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