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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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Control of synthetic microbial consortia in time, space, and composition

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Trends in Microbiology 2021年第12期29卷 1095-1105页

作者： Grandel, Nicolas E. Reyes Gamas, Kiara Bennett, Matthew R. Graduate Program in Systems Synthetic and Physical Biology Rice University Houston TX United States Department of Biosciences Rice University Houston TX United States Department of Bioengineering Rice University Houston TX United States

While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity. © 2021 Elsevier Ltd

关键词： control microbial consortia synthetic biology

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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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Prediction of cardiac differentiation in human induced pluripotent stem cell-derived cardiomyocyte supernatant using surface-enhanced Raman spectroscopy and machine learning

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Biosensors and Bioelectronics 2025年 283卷 117528页

作者： Echeverría-Altamar, Karla Barreto-Gamarra, Carlos Domenech-García, Maribella Resto-Irizarry, Pedro Bioengineering Graduate Program University of Puerto Rico at Mayagüez Mayagüez 00680 Puerto Rico Chemical Engineering Department University of Puerto Rico at Mayagüez Mayagüez 00680 Puerto Rico Mechanical Engineering Department University of Puerto Rico at Mayagüez Mayagüez 00680 Puerto Rico

The efficient manufacturing of cardiomyocytes from human-induced pluripotent stem cells (hiPSCs) is essential for advancing regenerative therapies for myocardial injuries. However, ensuring cell quality during production is challenging since traditional methods are invasive, destructive, and time-consuming. In this study, we monitored cardiomyocyte differentiation of WTC11 hiPSCs by analyzing conditioned media collected at various stages using Raman spectroscopy, multivariate analysis, and machine learning. Differentiation efficiency was confirmed via flow cytometry and immunostaining. Raman spectra were processed using standard normal variate and second derivative transformations before performing a principal component analysis (PCA) and machine learning (Random Forest, K-Nearest Neighbors, and Deep Neural Networks [DNN]). Results show that PCA was unable to distinguish cells based on differentiation stages, while machine learning could reliably predict cell differentiation early in the cardiac cell manufacturing process. DNN models achieved accuracies exceeding 82 % in predicting differentiation, highlighting their potential as quality control tools. These findings underscore the potential of Raman spectroscopy coupled with machine learning as a tool for real-time monitoring of cardiomyocyte production. © 2025 The Authors

关键词： Deep neural networks

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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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Multi-physics modeling and finite-element formulation of neuronal dendrite growth with electrical polarization

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Brain Multiphysics 2023年 4卷

作者： Wang, Shuolun Wang, Xincheng Holland, Maria A. Department of Aerospace and Mechanical Engineering University of Notre Dame Notre Dame 46556 IN United States Bioengineering Graduate Program University of Notre Dame Notre Dame 46556 IN United States

The neuron serves as the basic computational unit for the brain. Altered neuronal morphologies are usually found in various neurological diseases, such as Down syndrome, Williams syndrome, and idiopathic autism. Compelling biological evidence demonstrates that neuronal morphology can be dynamically regulated by neuronal activity through the mediation of calcium signaling pathways. Moreover, studies have revealed that exposure to an applied electric field can induce directional migration of neurites toward the cathode. In this study, we developed a coupled system that combines an advective Gray–Scott model with Gauss's law to gain a better understanding of dendrite growth and response to electrical polarization. Our simulation results successfully capture key features such as dendrite branching, space-filling, self-avoidance, and electrical polarization. With the help of the convolutional neural network, we inversely identified model parameters of real dendrite morphologies from an online open source. Finally, we calibrated our model using experimental data on growing neurons under applied electric fields. © 2023

关键词： Convolutional neural network Finite element modeling Neuronal dendrites Turing patterns

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Resistive-pulse sensing tumor-derived exosome detection device for resrouce-limited settings 21

Resistive-pulse sensing tumor-derived exosome detection devi...

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

作者： Carey, Thomas R. Yu, Connie W. Sohn, Lydia L. UC Berkeley-UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9780692941836

We present the theory, design, and initial characterization of a tumor-derived exosome detection platform based on resistive-pulse sensing to enable cost-effective, point-of-care cancer screening. Our platform detects exosomes displaying a specific surface antigen by electronically measuring the effective size increase that occurs when exosomes bind to colloids functionalized with a specific antibody. We have demonstrated that our device can distinguish antibody-functionalized colloids from similar colloids incubated with SKBR3-derived exosomes. © 17CBMS-0001.

关键词： Colloids

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Transferrin-Mediated Nanophotosensitizer to Enhance Phototherapy with Photoacoustic Imaging Under Hypoxia

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CCS Chemistry 2025年第4期7卷 1127-1141页

作者： Mengyao Yang Yunyoung Nah Donghyeon Oh Xingshu Li Heejeong Kim Sinyoung Park Junha Lim Aibing Chen Chulhong Kim Won Jong Kim Juyoung Yoon College of Chemical and Pharmaceutical Engineering Hebei University of Science and TechnologyShijiazhuang 050018 Department of Chemistry and Nanoscience Ewha Womans UniversitySeoul 03760 Department of Chemistry POSTECH-Catholic Biomedical Engineering InstitutePOSTECHPohang 37673 Department of Electrical Engineering Convergence IT EngineeringMechanical Engineeringand Medical Science and EngineeringMedical Device Innovation CenterPOSTECHPohang 37673 Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy College of ChemistryFuzhou UniversityFuzhou 350108 School of Interdisciplinary Bioscience and Bioengineering POSTECHPohang 37673 Graduate Program in Innovative Biomaterials Convergence Ewha Womans UniversitySeoul 03760

Various obstacles[poor tissue penetration,hypoxic tumor microenvironment,and reactive oxygen species(ROS)production quenching due to aggregation]obstruct imaging-guided high-efficiency phototherapy targeting ***,nanophthalocyanine(ZnPcN4-TF)is elaborately designed based on a synthetic phthalocyanine derivative(ZnPcN4)and nonimmunogenic transferrin(TF)through multiple noncovalent interactions for photoacoustic(PA)imaging-guided *** conjugating electron-rich amino groups effectively suppressed fluorescence and ROS generation due to the strong photoinduced electron transfer effect,ZnPcN4 became an ideal photothermal and PA imaging ***4-TF not only effectively targeted tumor sites and accumulated there,but also,surprisingly,facilitated the enhancement of ROS production via a type I process in an aggregate compared to ZnPcN4 itself,potentially due to accelerated electron ***,ZnPcN4-TF had a substantially more powerful photothermal effect than ZnPcN4 ***,this design effectively overcomes the obstacles to photodynamic therapy(aggregation-related ROS generation quenching in a hypoxic environment).Furthermore,PA imaging solves the tissue penetration challenge in optical *** study provides a broader base for designing novel photosensitizers to improve phototherapy under hypoxia.

关键词： photoacoustic imaging type I reactive oxygen species photothermal effect tumor accumulation self-assembly

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Fast non-iterative algorithm for 3D point-cloud holography

arXiv

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arXiv 2023年

作者： Ersaro, Nathan Tessema Yalcin, Cem Murray, Liz Kabuli, Leyla Waller, Laura Muller, Rikky Graduate Program in Bioengineering University of California Berkeley University of California San Francisco BerkeleyCA94720 United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA94720 United States

Recently developed iterative and deep learning-based approaches to computer-generated holography (CGH) have been shown to achieve high-quality photorealistic 3D images with spatial light modulators. However, such approaches remain overly cumbersome for patterning sparse collections of target points across a photoresponsive volume in applications including biological microscopy and material processing. Specifically, in addition to requiring heavy computation that cannot accommodate real-time operation in mobile or hardware-light settings, existing sampling-dependent 3D CGH methods preclude the ability to place target points with arbitrary precision, limiting accessible depths to a handful of planes. Accordingly, we present a non-iterative point cloud holography algorithm that employs fast deterministic calculations in order to efficiently allocate patches of SLM pixels to different target points in the 3D volume and spread the patterning of all points across multiple time frames. Compared to a matched-performance implementation of the iterative Gerchberg-Saxton algorithm, our algorithm's relative computation speed advantage was found to increase with SLM pixel count, reaching >100,000x at 512x512 array format. Copyright © 2023, The Authors. All rights reserved.

关键词： Iterative methods

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