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International Challenge on Segment Anything in Medical Images on Laptop held in conjunction with the IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2024

作者： Kong, Youngbin Kim, Kwangtai Jeong, Seoi Lee, Kyu Eun Kong, Hyoun-Joong Interdisciplinary Program in Bioengineering Graduate School Seoul National University Seoul Korea Republic of Department of Transdisciplinary Medicine Seoul National University Hospital Seoul Korea Republic of Department of Surgery Seoul National University Hospital and College of Medicine Seoul Korea Republic of Department of Medicine Seoul National University College of Medicine Seoul Korea Republic of Innovative Medical Technology Research Institute Seoul National University Hospital Seoul Korea Republic of Interdisciplinary Program of Medical Informatics Seoul National University College of Medicine Seoul Korea Republic of

ISBN: (纸本)9783031818530

Medical image segmentation is a crucial step for accurate diagnosis and treatment planning, as it provides quantitative information about anatomical structures and pathological lesions in various clinical scenarios. However, the existing methodologies have limitations in terms of their generalizability and computational efficiency. In this study, we propose SwiftMedSAM, an ultra-lightweight prompt-based general model, to enable efficient medical image segmentation even in resource-constrained environments. Based on LiteMedSAM, we significantly reduced the model size and computational complexity through the hyperparameter optimization of the image encoder and mask decoder components. SwiftMedSAM showed remarkable performance across various imaging modalities enabling real-time inference in resource-limited computing environments. It achieved a validation score of 0.75 demonstrating that SwiftMedSAM outperformed the existing methodologies in terms of the trade-off between accuracy and efficiency. Owing to its unprecedented generalizability and low computational cost, SwiftMedSAM is expected to enable high-quality medical image analysis in resource-constrained settings, thereby contributing to advancements in precision medicine and telemedicine. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Medical imaging

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COIN: Confidence Score-Guided Distillation for Annotation-Free Cell Segmentation

arXiv

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arXiv 2025年

作者： Jo, Sanghyun Lee, Seo Jin Lee, Seungwoo Hong, Seohyung Seo, Hyungseok Kim, Kyungsu OGQ Seoul Korea Republic of Laboratory of Cell & Gene Therapy Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University Korea Republic of Department of Biomedical Science and Medical Research Center College of Pharmacy Seoul National University Korea Republic of School of Transdisciplinary Innovations Interdisciplinary Program in Bioengineering Interdisciplinary Program in Artificial Intelligence Seoul National University Korea Republic of

Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research. While unsupervised CIS (UCIS) models aim to reduce the heavy reliance on labor-intensive image annotations, they fail to accurately capture cell boundaries, causing missed detections and poor performance. Recognizing the absence of error-free instances as a key limitation, we present COIN (COnfidence score-guided INstance distillation), a novel annotation-free framework with three key steps: (1) Increasing the sensitivity for the presence of error-free instances via unsupervised semantic segmentation with optimal transport, leveraging its ability to discriminate spatially minor instances, (2) Instance-level confidence scoring to measure the consistency between model prediction and refined mask and identify highly confident instances, offering an alternative to ground truth annotations, and (3) Progressive expansion of confidence with recursive self-distillation. Extensive experiments across six datasets show COIN outperforming existing UCIS methods, even surpassing semi- and weakly-supervised approaches across all metrics on the MoNuSeg and TNBC datasets. The code is available at https://***/shjo-april/COIN. © 2025, CC BY.

关键词： Semantic Segmentation

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YaleNLP @ PerAnsSumm 2025: Multi-Perspective Integration via Mixture-of-Agents for Enhanced Healthcare QA Summarization

arXiv

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arXiv 2025年

作者： Jang, Dongsuk Li, Alan Cohan, Arman Department of Computer Science Yale University United States Interdisciplinary Program for Bioengineering Seoul National University Korea Republic of Seoul National University Korea Republic of

Automated summarization of healthcare community question-answering forums is challenging due to diverse perspectives presented across multiple user responses to each question. The PerAnsSumm Shared Task was therefore proposed to tackle this challenge by identifying perspectives from different answers and then generating a comprehensive answer to the question. In this study, we address the PerAnsSumm Shared Task using two complementary paradigms: (i) a training-based approach through QLoRA fine-tuning of LLaMA-3.3-70B-Instruct, and (ii) agentic approaches including zero- and few-shot prompting with frontier LLMs (LLaMA-3.370B-Instruct and GPT-4o) and a Mixture-of-Agents (MoA) framework that leverages a diverse set of LLMs by combining outputs from multi-layer feedback aggregation. For perspective span identification/classification, GPT-4o zero-shot achieves an overall score of 0.57, substantially outperforming the 0.40 score of the LLaMA baseline. With a 2-layer MoA configuration, we were able to improve LLaMA performance up by 28% to 0.51. For perspective-based summarization, GPT-4o zero-shot attains an overall score of 0.42 compared to 0.28 for the best LLaMA zero-shot, and our 2-layer MoA approach boosts LLaMA performance by 32% to 0.37. Furthermore, in few-shot setting, our results show that the sentence-transformer embedding-based exemplar selection provides more gain than manually selected exemplars on LLaMA models, although the few-shot prompting is not always helpful for GPT-4o. The YaleNLP team’s approach ranked the overall second place in the shared task. Copyright © 2025, The Authors. All rights reserved.

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BPS2025 - Studying self-assembly of bacterial proteins in cell-free protein synthesis systems

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Biophysical Journal 2025年第3期124卷 55a-55a页

作者： Jacob B. Miller Nolan W. Kennedy Danielle Tullman-Ercek Carolyn E. Mills Interdisciplinary Biological Sciences Program Northwestern University Evanston IL USA Department of Chemical and Biological Engineering Northwestern University Evanston IL USA Department of Bioengineering University of California Santa Barbara Santa Barbara CA USA

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FET-based nanobiosensors for the detection of smell and taste

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Science China(Life Sciences) 2020年第8期63卷 1159-1167页

作者： Dongseok Moon Yeon Kyung Cha So-ong Kim Seongyeon Cho Hwi Jin Ko Tai Hyun Park School of Chemical and Biological Engineering Institute of Chemical ProcessesSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Program for Bioengineering Seoul National UniversitySeoul 08826Republic of Korea

Various nanobiosensors composed of biomaterials and nanomaterials have been developed,due to their demonstrated advantage of showing high *** various biomaterials for biological recognition elements of the nanobiosensor,sensory receptors,such as olfactory and taste receptors,are promising biomaterials for developing nanobiosensors,because of their high selectivity to target ***-effect transistors(FET)with nanomaterials such as carbon nanotube(CNT),graphene,and conducting polymer nanotube(CPNT),can be combined with the biomaterials to enhance the sensitivity of ***,many efforts have been made to develop nanobiosensors using biomaterials,such as olfactory receptors and taste receptors for detecting various smells and *** review focuses on the biomaterials and nanomaterials used in nanobiosensor systems and studies of various types of nanobiosensor platforms that utilize olfactory receptors and taste receptors which could be applied to a wide range of industrial fields,including the food and beverage industry,environmental monitoring,the biomedical field,and anti-terrorism.

关键词： nanobiosensor olfactory receptor taste receptor field-effect transistor(FET)

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High performance gamma-ray spectrometer based on Cs3Cu2I5 single crystal grown by room-temperature vacuum solvent-evaporation method

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Journal of Alloys and Compounds 2025年 1027卷

作者： Seo, Jiwon Song, Seungho Park, Minhwan Byun, Jangwon Park, Beomjun Park, Chansun Jang, Mee Yeom, Jung-Yeol Dept. of Health and Safety Convergence Science Korea University Seoul02841 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02841 Korea Republic of Dept. of Bioengineering Korea University Seoul02841 Korea Republic of Dept. of Materials Science and Engineering Korea University Seoul02841 Korea Republic of The Institute for High Technology Materials and Devices Korea University Seoul02841 Korea Republic of Global Health Technology Center Korea University Seoul02841 Korea Republic of Daejeon34057 Korea Republic of School of Biomedical Engineering Korea University Seoul02841 Korea Republic of

In this study, the properties of Cs3Cu2I5 (CCI) crystals grown using the Slow Vacuum Evaporation Technique (SVET) were examined. Crystals were grown at room temperature (300 K, 27 °C) under vacuum conditions, producing single crystals with maximum diameter of 13 mm over 23 days. We confirmed excellent crystallinity via X-ray diffraction (XRD), compositional uniformity via X-ray photoelectron spectroscopy (XPS), and homogeneity via electron probe micro analyzer (EPMA). UV-Vis measurements indicated a high transmittance of 83 % and a bandgap of 3.64 eV. The Stokes shift of 110 nm, smaller than previously reported values, contributed to faster decay times and improved low-energy detection feasibility. Time-resolved photoluminescence (TR-PL) showed a rapid decay component (4.1 ns), accounting for 95.11 % of the total decay, demonstrating superior properties compared to existing reports. The gamma-ray detection capabilities of the CCI crystals were evaluated using six radioactive sources (Am-241, Ba-133, Co-57, Na-22, Cs-137, and Mn-54), achieving excellent energy resolution, including 5.2 % at 662 keV. The crystals displayed a highly linear response to gamma radiation (R² = 0.99998) with a light yield of 55,613 photons/MeV. Moreover, assessments of multiple crystals grown under identical conditions showed consistent performance with a coefficient of variation (CV) of 1.23 %. These findings confirm that SVET is a highly effective and cost-efficient method for producing high-quality CCI crystals, offering significant advantages over other growth techniques. © 2025 Elsevier B.V.

关键词： Gamma ray spectrometers

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Verification of Geant4-DNA step-by-step-reaction-diffusion master equation model for long-term radiolysis simulation

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Physica Medica 2025年 133卷 104983-104983页

作者： Yoon, Euntaek Tran, Ngoc Hoang Incerti, Sebastien Choi, Chang Heon Interdisciplinary Program in Bioengineering Seoul National University Seoul 08826 Cuba Biomedical Research Institute Seoul National University Hospital Seoul 03080 Cuba Univ. Bordeaux CNRS LP2I UMR 5797 Gradignan F-33170 France Department of Radiation Oncology Seoul National University Hospital Seoul 03080 Cuba Institute of Radiation Medicine Seoul National University Medical Research Center Seoul 03080 Cuba Department of Radiation Oncology Seoul National University College of Medicine Seoul 03080 Cuba

Purpose: This paper describes the verification of the step-by-step-reaction-diffusion Master Equation (SBS-RDME) model, implemented in Geant4-DNA, for long-term radiolysis simulations in the Fricke dosimeter. Methods: Scaling for reaction rate constants due to the high acidity of the Fricke solution was applied. The secondary electrons generated by gamma irradiation from Co-60 were used as the radiation source for the simulations. Model parameters were optimized by observing changes in output and computation time in response to variations in the starting time t and initial voxel resolution ℎ of the compartment-based simulation. The yields of ferric ion G(Fe³⁺) and chemical species influencing its formation were calculated using the SBS-RDME model and using the IRT method for comparison. The time evolution of the yields of Fe³⁺, ^[rad]OH, H^[rad], HO₂^[rad], H₂O₂, and H₂ were compared, and the reactions affecting the yield of each chemical species were analyzed. Results: The model parameters were set to t = 5 ns and h = 12.5 nm. The yield trends over time for chemical species were consistent between the SBS-RDME model and the IRT method. At 50 s, the G(Fe³⁺) from the two calculations agreed within 3.2 %. Contribution analysis of the reactions affecting the generation/removal of each chemical species indicated that the main reason for this discrepancy between the two calculations might be the inability of the SBS method to consider specific reaction types during simulation. Conclusions: The SBS-RDME model was verified for long-term simulations by comparing its results to those obtained from the IRT method. © 2025 Associazione Italiana di Fisica Medica e Sanitaria

关键词： Fricke dosimetry Geant4-DNA RDME Water radiolysis

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A one-step pipetting platform for large-scale sequential drug combination assay with a network-based approach to cancer research 21

A one-step pipetting platform for large-scale sequential dru...

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21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017

作者： Kim, Su Deok Song, Seo Woo Oh, Dong Yoon Lee, Yongju Kwon, Sunghoon Electrical and Computer Engineering Seoul National University Korea Republic of Interdisciplinary Program of Bioengineering Seoul National University Korea Republic of

ISBN: (纸本)9780692941836

The importance of sequential drug combinations for therapeutic benefit has been demonstrated in recent years in that it can dynamically rewire signaling networks of a cancer cell over time. However, conventional methods of finding sequential pair out of numerous sequential combinations demands laborious work and high reagent cost. Here we report a novel handling technique of chemical substances using a combination of heterogeneous encoded drug-laden microparticles(DLPs) and a plastic microwell array with a rigid-body and pillar structure for easy assembly allowing sequential screening with ease without conventional numerous pipetting. We demonstrated its capability in large-scale sequential drug screening assay with reduced assay cost and time. © 17CBMS-0001.

关键词： Diseases

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In vitro Blood-brain barrier model using microfluidic platform 20

In vitro Blood-brain barrier model using microfluidic platfo...

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20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016

作者： Lee, S.M. Chung, M.H. Son, K.M. Jeon, N.L. Interdisciplinary Program for Bioengineering Seoul National University Korea Republic of School of Mechanical Engineering Seoul National University Korea Republic of

ISBN: (纸本)9780979806490

Blood-brain barrier (BBB) is neurovascular unit strictly controlling the exchange of nutrients and signals between neural and vascular system. Although critical roles of BBB on neural disease and drug delivery effectiveness has been issued lately, still the mechanism of barrier function and even their developmental process has not been clearly verified yet. Therefore some in vitro models were developed through the last decades but most of them could not satisfy both morphological and physiological properties to become a research model. Here we introduce a microfluidic platform which enables to co-culture three main cell types(endothelial cell, astrocyte and pericyte) comprising BBB in three dimensional (3D) hydrogel. Through our device, we could mimic neurovascular niche in its similar morphology and also physiological properties. Also we could verify that by quantifying increased expression of junctions and transportation systems related with barrier function.

关键词： Microfluidics

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3D vascular networks co-cultured with various types of colorectal cancer cells for validation of natural killer cell cytotoxicity 24

3D vascular networks co-cultured with various types of color...

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24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Choi, Hyeri Song, Jiyoung Park, Dohyun Jeon, Noo Li Interdisciplinary Program for Bioengineering Seoul National University Korea Republic of Departement of Mechanical Engineering Seoul National University Korea Republic of

ISBN: (纸本)9781733419017

Given that vascular networks are essential for the delivery of nutrients and oxygen during tumor progression, tumor models composed of blood vessels have been substantially needed in in vitro studies. Therefore, we developed a tumor vasculature model using various types of colorectal cancer cells on an injection-molded microfluidic platform. This model enabled high-throughput experiments and imaging, as well as demonstrated the typical characteristics of tumor vasculature including abnormality. The functional blood vessels are expected to be further used for delivering anticancer drugs to tumor sites or elucidating cytotoxic lymphocyte infiltration. © 2020 CBMS-0001

关键词： Microfluidics

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