Simon F. Nørrelykke

COPI Coatomer Regulates Several Steps of HDL Metabolism

Grigorios Panteloglou, Paolo Zanoni, Christopher S. Law, Brian Woods et autres

Abstract Background Reverse cholesterol transport by high density lipoproteins (HDL) is considered as an anti-atherogenic metabolic pathway. Hepatocytes determine the efficacy of this pathway by the production of apolipoprotein A-I (apoA-I) and its lipidation by ATP binding cassette transporter A1 (ABCA1), selective …

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Cancer-associated fibroblasts regulate DNA repair in pancreatic cancer through NDRG1-mediated R-loop processing

N. V. Kozlova, Kayla Cruz, Antoine A. Ruzette, Hanna M. Doh et autres

Pancreatic ductal adenocarcinomas (PDACs) are aggressive, stroma-rich tumours. They are unresponsive to treatments, and patients relapse quickly on DNA-damaging chemotherapies. PDAC stroma consists of extracellular matrix proteins (ECM), secreted by cancer-associated fibroblasts (CAFs). Here we show an unexpected link between CAF-secreted ECM …

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Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney

M. Diakova, Takaharu Ichimura, Ayumi Takakura, Ranit Karmakar et autres

Abstract Conventional histological relies on fixation, embedding, sectioning, and staining methods that distort cellular architecture, extract lipids, and introduces variability, limiting reproducibility. We present Normalized Stimulated Raman Imaging (NoRI) that enables quantitative, label-free protein and lipid measurements at high-spatial resolution. NoRI computationally …

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An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

Antoine A. Ruzette, N. V. Kozlova, Kayla Cruz, Taru Muranen et autres

Aggressive cancers, such as pancreatic ductal adenocarcinoma (PDAC), are often characterized by a complex and desmoplastic tumor microenvironment, a stroma rich supportive connective tissue composed primarily of extracellular matrix (ECM) and non-cancerous cells. Desmoplasia, a dense deposition of stroma, is a major …

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An Fc-SPINK1 fusion protein inhibits pancreatic inflammation in a mouse model

Jeffrey C. Way, Daniel Heid, M. Theiß, Simon F. Nørrelykke et autres

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SoftPQ: Robust Instance Segmentation Evaluation via Soft Matching and Tunable Thresholds

Ranit Karmakar, Simon F. Nørrelykke

Segmentation evaluation metrics traditionally rely on binary decision logic: predictions are either correct or incorrect, based on rigid IoU thresholds. Detection--based metrics such as F1 and mAP determine correctness at the object level using fixed overlap cutoffs, while overlap--based metrics like Intersection …

An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

Antoine A. Ruzette, N. V. Kozlova, Kayla Cruz, Taru Muranen et autres

1. Abstract Aggressive cancers, such as pancreatic ductal adenocarcinoma (PDAC), are often characterized by a complex and desmoplastic tumor microenvironment rich in stroma, a supportive connective tissue composed primarily of extracellular matrix (ECM) and non-cancerous cells. Desmoplasia, which is a dense deposition …

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A novel DNA repair protein, N-Myc downstream regulated gene 1 (NDRG1), links stromal tumour microenvironment to chemoresistance

Nina Kozlova, Kayla Cruz, Hanna M. Doh, Antoine A. Ruzette et autres

Abstract In pancreatic ductal adenocarcinoma cancer (PDAC) drug resistance is a severe clinical problem and patients relapse within a few months after receiving the standard-of-care chemotherapy. One contributing factor to treatment resistance is the desmoplastic nature of PDAC; the tumours are surrounded …

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The crucial role of bioimage analysts in scientific research and publication

Beth A. Cimini, Peter Bankhead, Rocco D’Antuono, Elnaz Fazeli et autres

Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality …

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Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser

Ishaant Agarwal, Joanna Kaczmar-Michalska, Simon F. Nørrelykke, Andrzej J. Rzepiela

Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. However, despite extensive processing of large image sets collected in cryo-EM experiments to amplify the signal-to-noise ratio, the reconstructed 3D protein-density maps are often limited in quality due to residual …

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Refinement of Cryo-EM 3D Maps with Self-Supervised Denoising Model: crefDenoiser

Ishaant Agarwal, Joanna Kaczmar-Michalska, Simon F. Nørrelykke, Andrzej J. Rzepiela

Abstract Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. Despite extensive processing of large image sets collected in a cryo-EM experiment to amplify the signal-to-noise ratio, the reconstructed 3D protein density maps are often limited in quality due …

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How Modifications of Corneal Cross-Linking Protocols Influence Corneal Resistance to Enzymatic Digestion and Treatment Depth

Malwina Kowalska, Elisa Mischi, Szymon Stoma, Simon F. Nørrelykke et autres

Purpose: The purpose of this study was to determine the effects of the Photoactivated Chromophore for Keratitis Corneal Cross-Linking (PACK-CXL) protocol modifications on corneal resistance to enzymatic digestion and treatment depth. Methods: Eight hundred one ex vivo porcine eyes were randomly divided …

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