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An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF).
Nat Protoc
January 2025
Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
Deep and accurate proteome analysis is crucial for understanding cellular processes and disease mechanisms; however, it is challenging to implement in routine settings. In this protocol, we combine a robust chromatographic platform with a high-performance mass spectrometric setup to enable routine yet in-depth proteome coverage for a broad community. This entails tip-based sample preparation and pre-formed gradients (Evosep One) combined with a trapped ion mobility time-of-flight mass spectrometer (timsTOF, Bruker).
View Article and Find Full Text PDFExploration of linear and interpretable models for quantification of cell parameters via contactless short-wave infrared hyperspectral sensing.
Sci Rep
January 2025
Fischell Department of Bioengineering, University of Maryland, College Park, USA.
The development of optical sensors for label-free quantification of cell parameters has numerous uses in the biomedical arena. However, using current optical probes requires the laborious collection of sufficiently large datasets that can be used to calibrate optical probe signals to true metabolite concentrations. Further, most practitioners find it difficult to confidently adapt black box chemometric models that are difficult to troubleshoot in high-stakes applications such as biopharmaceutical manufacturing.
View Article and Find Full Text PDFSimplified acid extraction and quantification of histones in human tumor cells.
Methods Cell Biol
January 2025
Department of Medical Biochemistry and Molecular Biology and Immunology, Medical School, Virgen Macarena University Hospital, University of Seville, Seville, Spain; Cancer Division, Faculty of medicine, Imperial college London, United Kingdom.
Histones are essential nuclear proteins that package eukaryotic DNA into chromosomes, play a vital role in gene regulation, DNA replication, DNA repair and chromosome condensation. Understanding histone modifications is crucial for grasping biological and disease-related processes. Specific alterations in histone modifications serve as sensitive and selective biomarkers for conditions like cancer, impacting both tumor and immune cells and affecting their interactions.
View Article and Find Full Text PDFKernel representation-based End-to-End network-enabled decoding strategy for precise and medical diagnosis.
J Hazard Mater
January 2025
School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430070, China; Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System, Wuhan 430070, China. Electronic address:
Artificial intelligence-assisted imaging biosensors have attracted increasing attention due to their flexibility, allowing for the digital image analysis and quantification of biomarkers. While deep learning methods have led to advancements in biomarker identification, the diversity in the density and adherence of targets still poses a serious challenge. In this regard, we propose CellNet, a neural network model specifically designed for detecting dense targets.
View Article and Find Full Text PDFArtificial Intelligence-Powered Human Epidermal Growth Factor Receptor 2 and Tumor Microenvironment Analysis in Human Epidermal Growth Factor Receptor 2-Amplified Metastatic Colorectal Cancer: Exploratory Analysis of Phase II TRIUMPH Trial.
JCO Precis Oncol
January 2025
Translational Research Support Office, National Cancer Center Hospital East, Chiba, Japan.
Purpose: Human epidermal growth factor receptor 2 (HER2)-targeted therapies have shown promise in treating -amplified metastatic colorectal cancer (mCRC). Identifying optimal biomarkers for treatment decisions remains challenging. This study explores the potential of artificial intelligence (AI) in predicting treatment responses to trastuzumab plus pertuzumab (TP) in patients with -amplified mCRC from the phase II TRIUMPH trial.
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