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Rath, J.

Publications and source records attributed to Rath, J..

3 recordsLinked to original sources

DCGAN-Based Synthetic MRI Augmentation for Data-centric Brain Tumor Segmentation

Accurate brain tumor segmentation from magnetic resonance imaging (MRI) remains a challenging task because supervised deep learning models require large quantities of annotated data, which are expensive and time-consuming to obtain. This study investigates whether synthetic MRI images generated using a Deep Convolutional Generative Adversarial Network (DCGAN) can improve U-Net-based brain tumor segmentation using synthetic data augmentation. Experiments were performed on the LGG-MRI dataset comprising 3,929 image-mask pairs. A baseline U-Net was first trained using the original training dataset. Synthetic MRI images were subsequently generated using a DCGAN, and threshold-derived pseudo-masks were assigned to the generated images to construct an augmented training dataset. The same U-Net architecture was then retrained using the augmented dataset and evaluated on an identical held-out test set. Compared with the baseline model, DCGAN-based augmentation increased the Dice coefficient from 0.2067 to 0.3037 and the Intersection over Union (IoU) from 0.1243 to 0.1918, while reducing the final test loss from 0.0474 to 0.0275. These results indicate that synthetic MRI augmentation was associated with improved segmentation performance under the experimental conditions of this study. However, the reliance on threshold-derived pseudo-labels and evaluation on a single dataset limit the generalizability of the results. The proposed workflow provides a reproducible implementation for evaluating DCGAN-based synthetic data augmentation in supervised brain tumor segmentation and establishes a baseline for future studies employing more reliable annotation strategies and broader experimental validation.

bioengineering↗

Unveiling the Molecular Architecture of T Cells and Immune Synapses with Cryo-Expansion Microscopy

Cellular communication is critical for anti-cancer immunity, with tumor cell killing occurring at immunological synapses (IS) formed between effector immune cells and target tumor cells. While optical super-resolution microscopy (SRM) has enlightened the spatial organization of the IS mostly in regular immune cells, visualizing the nanoscale architectural features of IS in its native state, including 3D receptor distribution and the ultrastructural details of the lytic granule release remains challenging. Using cryo-expansion microscopy (cryo-ExM), we unravel the cellular architecture of activated T cells and T cell-target cell pairs. Our approach visualizes actin and microtubule networks during synapse formation, membrane topography, and the distribution of signaling molecules and lytic granules of different types, offering novel insights into IS organization. Finally, we apply U-ExM to glioblastoma tissue, visualizing T cells and their lytic content in situ, highlighting its potential for pre-clinical immunotherapy studies.

immunology↗

Carbon nanoparticle exposure strengthens water-relation parameters by stimulating abscisic acid pathway and aquaporins genes in rice

Mechanism of action and molecular basis of positive growth effects including yield increase due to carbon nanoparticle (CNP) treatment in rice plants is dissected here. CNP at 500 -750 {micro}g/mL were found to be the optimum dosages showing best seedling growth. CNP treatment resulted increase in stomata size, gaseous exchange and water use efficiency along with decrease in stomata frequency, relative humidity, internal CO2 concentration. CNP treatment exerted cold tolerance in seedlings and water stress tolerance in reproductive stage. CNP-coupled with water uptake was found to be endocytosis mediated, although CNP uptake was not affected by endocytosis inhibitor application in roots. Genomic analysis resulted major involvement of ABA pathway and stomata size and frequency genes in Arabidopsis and rice. Elevated endogenous ABA in rice seedlings and flag leaves along with increased expression of ABA biosynthetic genes in Arabidopsis and rice AtNCED3, AtNCED6, OsNCED1 confirmed increased ABA synthesis. Negative regulators of ABA pathway, OsSNRK2 down-regulation and up-regulation of stomagen (OsEPFL9) reconfirmed ABAs involvement. CNP treatment resulted water stress tolerance by maintaining lower stomatal conductance, transpiration rate and higher relative water content. Increased ABA (OsSNRK1, OsSNRK2) and aquaporin (OsPIP2-5) genes expressions could explain the better water stress tolerance in rice plants treated with CNP. Altogether, due to thermomorphogenesis, down-regulation of Phytochrome B resulted altered the ABA pathway and stomatal distribution with size. These changes resulted improved water relation parameters and WUE showing improvement in yield. Detailed mechanism of action of CNP in abiotic stress tolerance can be exploited in in nano-agriculture.

plant biology↗