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Mogulkoc, N.

Publications and source records attributed to Mogulkoc, N..

2 recordsLinked to original sources

Multiscale mapping of venous remodelling in idiopathic pulmonary fibrosis

The integrity of the pulmonary vasculature is a key determinant of lung health, yet challenges in visualisation and quantification have hindered interrogation of its pathophysiological role in chronic lung disease. Here, we align recent advances in microscale image acquisition with novel computer vision-based vessel segmentation models to demonstrate expansion of the bronchial and pulmonary veins across varying severities of tissue remodelling in idiopathic pulmonary fibrosis (IPF). Relating these imaging findings to molecular data in control, mild, and severe fibrosis, we show that bronchial venous endothelial cells expand beyond their physiological peribronchial niche even in mild disease, acquiring persistent angiogenic, inflammatory, and matrix-remodelling programmes that define a specialised fibrovascular-immune interface. Finally, we relate these microscale and molecular observations to clinical CT imaging, demonstrating that intrapulmonary vein enlargement independently associates with worsened survival across three IPF cohorts. Collectively, our multimodal, multiscale approach connects previously unresolved three-dimensional venous architecture to its molecular endothelial correlate, establishing venous enlargement as a prognostically significant and clinically relevant feature of IPF. Our analytical approach also demonstrates how biological discoveries made in intact ex vivo human organs can translate into measurable phenotypes in living patients, providing a template for other organs and diseases.

pathology↗

Tube2FEM: a general-purpose highly-automated pipeline for flow related processes in (embedded) tubular objects

This paper presents a comprehensive and highly-automated open-source pipeline for simulating flow and flow-related processes in (embedded) tubular structures. Addressing a critical gap in computational fluid dynamics (CFD) and simulation sciences, it facilitates the transition from raw three-dimensional imaging, graph networks, or CAD models of tubular objects to refined, simulation-ready meshes. This transition, traditionally labor-intensive and challenging, is streamlined and highly-automated through a series of innovative steps that include surface mesh processing, centre-line construction, anisotropic mesh generation, and volumetric meshing, leading to Finite Element Method (FEM) simulations. The pipeline leverages a range of open-source software and libraries, notably GIBBON, FEniCS, and Paraview, to provide flexibility and broad applicability across different simulation scenarios, ranging from biomedical to industrial applications. We demonstrate the versatility of our approach through five distinct applications, including the mesh generation for soil-root systems, lung airways, microcirculation networks, and portal vein networks, each originating from a different data source. Moreover, for several of these cases, we incorporate Computational Fluid Dynamics (CFD) simulations and strategies for 3D-1D coupling between the embedding domain and the embedded structures. Finally, we outline some future perspectives aimed at enhancing accuracy, reducing computational time, and incorporating advanced modeling and boundary condition strategies to further refine the frameworks capabilities.

bioengineering↗