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Computational Optical Sensing and Imaging, COSI 2021 - Part of OSA Imaging and Applied Optics Congress 2021

作者： Shuai, Richard W. Yanny, Kyrollos Monakhova, Kristina Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We present a deep-learning method based on Wiener filters and U-Nets that performs image reconstruction in systems with spatially-varying aberrations. We train on simulated microscopy measurements and test on experime... 详细信息

ISBN: (纸本)9781557528209

关键词： Image reconstruction

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SAME-CELL, SINGLE-CELL DETECTION OF PROTEIN ISOFORMS AND NUCLEIC ACIDS 25

SAME-CELL, SINGLE-CELL DETECTION OF PROTEIN ISOFORMS AND NUC...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Gomez Martinez, Ana E. Rosas-Canyelles, Elisabet Modzelewski, Andrew J. Geldert, Alisha Gopal, Anjali He, Lin Herr, Amy E. Department of Bioengineering University of California Berkeley BerkeleyCA United States UC Berkeley-UCSF Graduate Program in Bioengineering United States Division of Cellular and Developmental Biology Department of Molecular & Cell Biology University of California BerkeleyCA United States

ISBN: (纸本)9781733419031

Single-cell 'omics is advancing rapidly, but there are gaps in linking nucleic acids to proteins in their myriad forms. To surmount this gap, we describe a microfluidic device that reports information on nucleic acids and proteoforms, or proteins that arise from a variety of modifications to nucleic acids or proteins, which are detected by immunoblotting (triBlot). The triBlot fractionates nuclei from the cytoplasm, allowing analysis of cytoplasmic proteoforms. Then, nuclei-laden regions are laser excised to perform PCR/RT-qPCR. We correlate DNA, mRNA, and protein expression from the same few cells, a step forward in 'omics that measure diverse protein forms. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Proteins

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Data Format Standardization and DICOM Integration for Hyperpolarized 13C MRI

arXiv

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arXiv 2024年

作者： Diaz, Ernesto Sriram, Renuka Gordon, Jeremy W. Sinha, Avantika Liu, Xiaoxi Sahin, Sule Crane, Jason Olson, Marram P. Chen, Hsin-Yu Bernard, Jenna Vigneron, Daniel B. Wang, Zhen Jane Xu, Duan Larson, Peder E.Z. Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley United States University of California San FranciscoCA United States

Hyperpolarized (HP) 13C MRI has shown promise as a valuable modality for in vivo measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard. This includes proposing a set of minimum set of information that is specific to HP 13C MRI studies. We then show where the majority of these can be fit into existing DICOM Attributes, primarily via the "Contrast/Bolus" module. We also demonstrate pipelines for utilizing DICOM for HP 13C MRI. DICOM is the most common standard for clinical medical image storage and provides the flexibility to accommodate the unique aspects of HP 13C MRI, including the HP agent information but also spectroscopic and metabolite dimensions. The pipelines shown include creating DICOM objects for studies on human and animal imaging systems with various pulse sequences. We also show a python-based method to efficiently modify DICOM objects to incorporate the unique HP 13C MRI information that is not captured by existing pipelines. Moreover, we propose best practices for HP 13C MRI data storage that will support future multi-site trials, research studies and technical developments of this imaging technique. © 2024, CC BY.

关键词： Magnetic resonance imaging

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Feasibility Assessment of a 3D Radiomicroscope for Charged Particles by Monte Carlo Simulation

Feasibility Assessment of a 3D Radiomicroscope for Charged P...

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： H. Chu J.S. Lee Interdisciplincary Program in Bioengineering Seoul National University Graduate School Seoul Republic of Korea Integrated Major in Innovative Medical Science Seoul National University Graduate School Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Seoul Republic of Korea

In this paper, we propose the new concept of 3D lensless radiomicrosope for charged particle by simulation. Applying the principle of lensless imaging and thin phosphor films as scintillator with directional guide, this imaging technique enables information of position and energy in optical pixel array. 2D autoradiograph images including this information were acquired at specific angles. Two beta emission sources are placed in different part of tissue, and these two sources are distinguished by intensity of pixels. In addition, the intensity difference between two sources discriminates as the placement of optical interface differs. Effects of directional information given by two phosphor films has also been verified by measuring of gaussian fitting curve of events on phosphor film compositions. In perspective of optical sensor application in real, fluorine-18 source activity was calculated by short video and estimated the exponential decay curve. The curve showed similar tendency with reference F-18 source. The results reveal that 3D lensless radiomicroscope method can work as another method to capture the beta emission information by utilizing simple optical source. The simulation result demonstrates that this method is practically feasible.

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Dynamic Threshold Discriminator - Mutual Learning for Scalable Time Stamping Neural Networks

Dynamic Threshold Discriminator - Mutual Learning for Scalab...

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： S. Bae M. Yi J.S. Lee Seoul National University Graduate School Interdisciplinary Program in Bioengineering Seoul Republic of Korea Seoul National University Graduate School Integrated Major in Innovative Medical Science Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Seoul Republic of Korea

The precision of emission image estimation relies on accurate interaction time estimation, which is becoming increasingly possible with neural network-based time stamping methods. In order to expand the use of these methods to multiple detector systems and facilitate mutual training, we leverage the inherent variance-bias characteristics of scintillator detectors. Our neural network, called the Dynamic Threshold Discriminator (DTD), is designed to estimate appropriate thresholds for given waveforms rather than estimating time stamps directly to exploit the characteristic. We assessed the feasibility of DTD using experimental data and compared it to classical time stamping methods (LED, CFD, LED with energy correction) and a neural network-based time stamping method. The proposed method showed a 12% lower coincidence timing resolution compared to LED with energy correction for a 500 keV energy window even without energy information and demonstrated robust performance regardless of the digitizer's sampling rate.

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Segmented readout for Cherenkov time-of-flight positron emission tomography detectors based on bismuth germanate

arXiv

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arXiv 2024年

作者： Yi, Minseok Lee, Daehee Gola, Alberto Merzi, Stefano Penna, Michele Lee, Jae Sung Cherry, Simon R. Kwon, Sun Il Department of Biomedical Engineering University of California Davis United States Interdisciplinary Program in Bioengineering College of Engineering Seoul National Graduate School Korea Republic of Integrated Major in Innovative Medical Science Seoul National Graduate School Korea Republic of Fondazione Bruno Kessler Italy Brightonix Imaging Inc. Korea Republic of

Positron emission tomography (PET) is the most sensitive biomedical imaging modality for noninvasively detecting and visualizing positron-emitting radiopharmaceuticals within a subject. In PET, measuring the time-of-flight (TOF) information for each pair of 511-keV annihilation photons improves effective sensitivity but requires high timing resolution. Hybrid materials that emit both scintillation and Cherenkov photons, such as bismuth germanate (BGO), recently offer the potential for more precise timing information from Cherenkov photons while maintaining adequate energy resolution from scintillation photons. However, a significant challenge in using such hybrid materials for TOF PET applications lies in the event-dependent timing spread caused by the mixed detection of Cherenkov and scintillation photons due to relatively lower production of Cherenkov photons. This study introduces an innovative approach by segmenting silicon photomultiplier (SiPM) pixels coupled to a single crystal, rather than using traditional SiPMs that are as large as or larger than the crystals they read. We demonstrated that multiple time stamps and photon counts obtained from the segmented SiPM can classify events by providing temporal photon density, effectively addressing this challenge. The approach and findings would lead to new opportunities in applications that require precise timing and photon counting, spanning the fields of medical imaging, high-energy physics, and optical physics. © 2024, CC BY.

关键词： Photons

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Investigation of Methodologies for Extracting Individual Brain Oscillations: Comparisons & Insights

Investigation of Methodologies for Extracting Individual Bra...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Xuanteng Yan Marie-Hélène Boudrias Georgios D. Mitsis Graduate Program in Biological and Biomedical Engineering McGill University Montréal Canada School of Physical & Occupational Therapy McGill University Montréal Canada Department of Bioengineering McGill University Montréal Canada

There is increasing evidence that the effects of non-invasive brain stimulation can be maximized when the applied intervention matches internal brain oscillations. Extracting individual brain oscillations is thus a necessary step for implementing personalized brain stimulation. In this context, different methods have been proposed for obtaining subject-specific spectral peaks from electrophysiological recordings. However, comparing the results obtained using different approaches is still lacking. Therefore, in the present work, we examined the following methodologies in terms of obtaining individual motor-related EEG spectral peaks: fast Fourier Transform analysis, power spectrum density analysis, wavelet analysis, and a principal component based time-frequency analysis. We used EEG data obtained when performing two different motor tasks – a hand grip task and a hand opening- and-closing task. Our results showed that both the motor task type and the specific method for performing the analysis had considerable impact on the extraction of subject-specific oscillation spectral *** Relevance—This exploratory study provides insights into the potential effects of using different methods to extract individual brain oscillations, which is important for designing personalized brain-machine-interfaces.

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Adaptive Environment-Aware Robotic Arm Reaching Based on a Bio-Inspired Neurodynamical Computational Framework

Adaptive Environment-Aware Robotic Arm Reaching Based on a B...

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IEEE International Workshop on Robot and Human Communication (ROMAN)

作者： Dimitrios Chatziparaschis Shan Zhong Vasileios Christopoulos Konstantinos Karydis Dept. of Electrical and Computer Engineering Univ. of California Riverside Riverside CA USA Neuroscience Graduate Program Univ. of California Riverside Riverside CA USA Dept. of Bioengineering Univ. of California Riverside Riverside CA USA

ISBN: (数字)9798350375022

ISBN: (纸本)9798350375039

Bio-inspired robotic systems are capable of adaptive learning, scalable control, and efficient information processing. Enabling real-time decision-making for such systems is critical to respond to dynamic changes in the environment. We focus on dynamic target tracking in open areas using a robotic six-degree-of-freedom manipulator with a bird-eye view camera for visual feedback, and by deploying the Neurodynamical Computational Framework (NeuCF). NeuCF is a recently developed bio-inspired model for target tracking based on Dynamic Neural Fields (DNFs) and Stochastic Optimal Control (SOC) theory. It has been trained for reaching actions on a planar surface toward localized visual beacons, and it can retarget or generate stop signals on the fly based on changes in the environment (e.g., a new target has emerged, or an existing one has been removed). We evaluated our system over various target-reaching scenarios. In all experiments, NeuCF had high end-effector positional accuracy, generated smooth trajectories, and provided reduced path lengths compared with a baseline cubic polynomial trajectory generator. In all, the developed system offers a robust and dynamic-aware robotic manipulation approach that affords real-time decision-making.

关键词： Visualization Accuracy Target tracking Robot vision systems Real-time systems Polynomials Generators Trajectory Robots Manipulator dynamics

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Integrating Chain-of-Thought and Retrieval Augmented Generation Enhances Rare Disease Diagnosis from Clinical Notes

arXiv

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arXiv 2025年

作者： Wu, Da Wang, Zhanliang Nguyen, Quan Wang, Kai Raymond G. Perelman Center for Cellular and Molecular Therapeutics Children's Hospital of Philadelphia PhiladelphiaPA19104 United States Applied Mathematics and Computational Science Graduate Program University of Pennsylvania PhiladelphiaPA19104 United States Bioengineering Graduate Program University of Pennsylvania PhiladelphiaPA19104 United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104 United States

Background: Several studies show that large language models (LLMs) struggle with phenotype-driven gene prioritization for rare diseases. These studies typically use Human Phenotype Ontology (HPO) terms to prompt foundation models like GPT and LLaMA to predict candidate genes. However, in real-world settings, foundation models are not optimized for domain-specific tasks like clinical diagnosis, yet inputs are unstructured clinical notes rather than standardized terms. How LLMs can be instructed to predict candidate genes or disease diagnosis from unstructured clinical notes remains a major challenge. Methods: We introduce RAG-driven CoT and CoT-driven RAG, two methods that combine Chain-of-Thought (CoT) and Retrieval Augmented Generation (RAG) to analyze clinical notes. A five-question CoT protocol mimics expert reasoning, while RAG retrieves data from sources like HPO and OMIM (Online Mendelian Inheritance in Man). We evaluated these approaches on rare disease datasets, including 5,980 Phenopacket-derived notes, 255 literature-based narratives, and 220 in-house clinical notes from Children’s Hospital of Philadelphia. Results: We found that recent foundations models, including Llama 3.3-70B-Instruct and DeepSeek-R1-Distill-Llama-70B, outperformed earlier versions such as Llama 2 and GPT-3.5. We also showed that RAG-driven CoT and CoT-driven RAG both outperform foundation models in candidate gene prioritization from clinical notes;in particular, both methods with DeepSeek backbone resulted in a top-10 gene accuracy of over 40% on Phenopacket-derived clinical notes. RAG-driven CoT works better for high-quality notes, where early retrieval can anchor the subsequent reasoning steps in domain-specific evidence, while CoT-driven RAG has advantage when processing lengthy and noisy notes. Conclusions: Integrating CoT and RAG enhances LLMs’ understanding of clinical notes in the context of rare disease diagnosis, and can facilitate various downstream medical tasks. © 2025, CC

关键词： Chains

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High-performance solid-solution potassium-ion intercalation mechanism of multilayered turbostratic graphene nanosheets

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Journal of Energy Chemistry 2022年第4期31卷 814-823页

作者： Jiae Um Seung Uk Yoon Hoseong Kim Beom Sik Youn Hyoung-Joon Jin Hyung-Kyu Lim Young Soo Yun Program in Environmental and Polymer Engineering Inha Universityncheon 22212 South Korea Department of Polymer Science and Engineering Inha UniversityIncheon 22212South Korea Division of Chemical Engineering and Bioengineering Kangwon National University Chuncheon Gangwon-do 24341 South Korea KU-KIST Graduate School of Converging Science and Technologyea University 145 Anam-roSeongbuk-guSoul02841 South Korea Department of Integrative Energy Engineering 145 Anam-roSongbuk-guKorea UniversitySeoul 02841 South Korea

The solid-solution reaction between an alkali cation and an active host material is known as a singlephase redox mechanism,and it is typically accompanied by a continuous voltage *** is distinct from the typical alkali cation intercalation reaction at an equivalent site of the active host material,which exhibits a voltage ***,we report an unusual solid-solution potassium-ion intercalation mechanism with a low-voltage plateau capacity on multilayered turbostratic graphene nanosheets(T-GNSs).Despite the disordered graphitic structure with a broad range of d-spacings(3.65–4.18À),the T-GNSs showed a reversible plateau capacity of~200 m A h g^(-1),which is higher than that of a well-ordered graphite nanoplate(~120 m A h g^(-1)).In addition,a sloping capacity of~220 m A h g^(-1)was delivered with the plateau capacity,and higher rate capabilities,better reversibility,and a more stable cycling performance were confirmed on the turbostratic ***-principles calculations suggest that the multitudinous lattice domains of the T-GNSs contain diverse intercalation sites with strong binding energies,which could be the origin of the high-performance solid-solution potassium-ion intercalation behavior when the turbostratic graphene stacks have a d-spacing smaller than that of equilibrium potassium–graphite intercalation compounds(5.35À).

关键词： Turbostratic graphite Graphene nanosheet Defective carbon Anode Potassium-ion batteries

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