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Improving Interpretability of Radiology Report-based Pediatric Brain Tumor Pathology Classification and Key-phrases Extraction Using Large Language Models

Improving Interpretability of Radiology Report-based Pediatr...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Chen Zhao Kareem Kudus Sara Ketabi Khashayar Namdar Matthias W. Wagner Birgit B. Ertl-Wagner Farzad Khalvati Department of Mechanical and Industrial Engineering University of Toronto Toronto ON Canada Neurosciences & Mental Health Research Program Research Institute The Hospital for Sick Children Toronto ON Canada Institute of Medical Science University of Toronto Toronto ON Canada Department of Diagnostic & Interventional Radiology The Hospital for Sick Children Toronto ON Canada Institute of Diagnostic and Interventional Neuroradiology University Hospital Augsburg Germany Department of Medical Imaging University of Toronto Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada

ISBN: (数字)9798350351552

ISBN: (纸本)9798350351569

Radiology reports are crucial for bridging the expertise of radiologists and other clinicians. Machine Learning models trained on these reports have shown promising performance in various downstream clinical tasks, such as predicting the necessity of future follow-up procedures, based on past radiology reports. However, for clinicians to adopt these models and for radiologists to validate the results, interpretability of the model is essential. In this study, we train BERT models on radiology reports to classify pediatric brain tumor pathologies. These large language models enable accurate report-level classification, without the need for costly word-level annotations. To identify and extract keywords and key-phrases related to distinct pathologies from radiology reports, we used a modified Term Frequency-Inverse Document Frequency to determine phrase importance based on prevalence and attributions scores. We achieved an overall multiclass Area Under Receiver Operating Characteristic Curve (AUROC) of 79.57% using ClinicaiBERT. Moreover, the per-class AUROC values were 86%, 71.2%, and 81.5%, for ‘Pilocytic Astrocytoma’, ‘Low-Grade Astrocytoma’, and ‘Other’ pathologies, respectively. Our explainability analysis identified hypotonia and mesencephalon as the most important terms for ‘Pilocytic Astrocytoma’ and ‘Low-Grade Astrocytoma’, respectively.

关键词： Pathology Annotations Large language models Brain tumors Receivers Radiology Predictive models Brain modeling Midbrain Radiofrequency identification

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Development and evaluation of a hand exoskeleton for finger rehabilitation

Development and evaluation of a hand exoskeleton for finger ...

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2022 IEEE International Conference on Robotics and Biomimetics, ROBIO 2022

作者： Luo, Haiyi Sun, Zhenyu Jing, Xiaobei Shu, Bairui Chen, Shixiong Yong, Xu Yokoi, Hiroshi Department of Mechanical Engineering and Intelligent Systems The University of Electro-Communications 1-5-1 Chofugaoka Tokyo Chofu182-8585 Japan CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen518055 China Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen518055 China Center for Neuroscience and Biomedical Engineering The University of Electro-communications 1-5-1 Chofugaoka Tokyo Chofu182-8585 Japan

ISBN: (纸本)9781665481090

Exoskeleton robots are now prevalent in hand rehabilitation medical training, and they can effectively drive a variety of rehabilitative movements in a hand that has lost its motor ability. To adapt to the hand's physiological structure and motion characteristics, a hybrid-driven exoskeleton hand based on tendon rope and linkage and its validation experiments are proposed in this paper. The exoskeleton hand can assist one to five fingers independently or even assist a joint alone. Wearing the robot retains the physiological touch of the hand to the maximum extent, which is beneficial to rehabilitation. In addition, patients can also carry out rehabilitation training independently, and the control mode is simple and practical. To verify whether the exoskeleton can reach the grip standard of healthy hands, the Leap Motion Controller is also used to conduct experimental verification of finger movement wearing the exoskeleton. The results show that the maximum average differences between the angles of the finger flexion motion joints (MCP and PIP) with and without the exoskeleton are 10.33 degrees and 11.06 degrees. It was verified that the exoskeleton could meet the requirements of finger flexion and extension for assisted motion within a specific error range. © 2022 IEEE.

关键词： Physiology

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Quantifying the acoustic field in a microchannel using microswimmers as measurement probes 24

Quantifying the acoustic field in a microchannel using micro...

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

作者： Kim, Minji Barnkob, Rune Mark Meacham, J. Department of Mechanical Engineering and Materials Science Washington University in St. Louis St. LouisMO63130 United States Heinz-Nixdorf-Chair of Biomedical Electronics Department of Electrical and Computer Engineering Technical University of Munich Munich81675 Germany

ISBN: (纸本)9781733419017

Rapid and accurate experimental characterization tools can advance development of acoustic microfluidic devices. We previously reported qualitative mapping of acoustic pressure fields using living microswimmers as active probes.1 Here, we apply this method for quantitative measurement of the acoustic energy density as an alternative to conventional particle tracing. Mass density and compressibility of motile Chlamydomonas reinhardtii (CR) algae cells were measured. The acoustic energy density within a straight microchannel driven at the first half-wavelength resonance was then calculated using the balance of swimming and acoustic radiation forces. Measurements are nearly equivalent to those obtained using acoustophoretic migration of passive particles. © 2020 CBMS-0001

关键词： Acoustic fields

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Polyelectrolyte-coated liposomes microfluidically assembled in one-step for enhancing cell endocytosis and in-vivo immune responses

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Colloids and Surfaces B: Biointerfaces 2024年 241卷 114030页

作者： Chen, Xin-an Chuang, Chuan-chang Chen, Cheng-cheung Lee, Chia-ying Chin, Chia-ying Young, Jenn-jong Bai, Meng-yi Chuang, Chuan-chung Biomedical Engineering Program Graduate Institute of Applied Science and Technology National Taiwan University of Science and Technology Taipei City10607 Taiwan Institute of Preventive Medicine National Defense Medical Center New Taipei City23742 Taiwan Department and Graduate Institute of Microbiology and Immunology National Defense Medical Center Taipei City11490 Taiwan Graduate Institute of Medical Sciences National Defense Medical Center Taipei City11490 Taiwan Adjunct Appointment to the Department of Biomedical Engineering National Defense Medical Center Taipei City11490 Taiwan School of Dentistry and Graduate Institute of Dental Science National Defense Medical Center Taipei City11490 Taiwan Department of dentistry Tri-Service General Hospital Taipei City11490 Taiwan

To enhance the cellular uptake of liposomes, we prepared conventional liposomes with targeting molecules and surface-charged liposomes and evaluated their potential as nano-carriers and vaccine adjuvants by comparing their endocytosis efficiencies using immune cells. Surface-charged liposomes were synthesized via a one-step microfluidic method, which provided a novel, simple, fast, and highly reproducible method for preparing liposomes. Flow cytometry revealed that cationic polyelectrolyte-coated liposomes exhibited higher endocytosis efficiencies (of up to a factor of 100) in A774A.1 cells and JAWs II cells compared with uncoated liposomes or those coated with anionic polyelectrolytes. Positively charged liposomes exhibited some cytotoxicity at quaternary-chitosan coating concentrations higher than 6 mg/mL;however, significantly lower cytotoxicities (by a factor of almost ten) were obtained by protein mixing. Furthermore, BALB/c mice vaccinated with a mixture of Anthrax vaccine adsorbed (AVA) and quaternary chitosan-coated liposomes showed faster and stronger anti-PA IgG inductions compared to those vaccinated with AVA alone, with titers positively correlating with the amount of cationic liposome used. This finding clearly reveals that quaternary chitosan-coated liposomes act as both nano-carriers and vaccine adjuvants that significantly enhance in-vivo immune responses to vaccines with low immunogenicities. © 2024 Elsevier B.V.

关键词： Polyelectrolytes

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Structural changes induced by electric currents in a single crystal of Pr2CuO4

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Physical Review Materials 2023年第8期7卷 083803-083803页

作者： Susmita Roy Feng Ye Zachary Morgan Kabir Mathur Anish Parulekar Syed I. A. Jalali Yu Zhang Gang Cao Nobu-Hisa Kaneko Martin Greven Rishi Raj Dmitry Reznik Department of Physics University of Colorado at Boulder Boulder Colorado 80309 USA Neutron Scattering Division Oak Ridge National Laboratory Oak Ridge Tennessee 37830 USA Materials Science and Engineering Program Department of Mechanical Engineering University of Colorado Boulder Boulder Colorado 80309 USA National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8563 Japan School of Physics and Astronomy University of Minnesota Minneapolis Minnesota 55455 USA Center for Experiments on Quantum Materials University of Colorado at Boulder Boulder Colorado 80309 USA

We demonstrate an approach to the structural and electronic property modification of perovskites, focusing on Pr2CuO4, an undoped parent compound of a class of electron-doped copper-oxide superconductors. Currents were passed parallel or perpendicular to the copper oxygen layers with the voltage ramped up until a rapid drop in the resistivity was achieved, a process referred to as “flash.” The current was then further increased tenfold in current-control mode. This state was quenched by immersion into liquid nitrogen. Flash can drive many compounds into different atomic structures with new properties, whereas the quench freezes them into a long-lived state. Single-crystal neutron diffraction of as-grown and modified Pr2CuO4 revealed a 10×10 superlattice due to oxygen-vacancy order. The diffraction peak intensities of the superlattice of the modified sample were significantly enhanced relative to the pristine sample. Raman-active phonons in the modified sample were considerably sharper. Measurements of electrical resistivity, magnetization, and two-magnon Raman scattering indicate that the modification affected only the Pr-O layers, but not the Cu-O planes. These results point to enhanced oxygen-vacancy order in the modified samples well beyond what can be achieved without passing electrical current. Our work opens a new avenue toward electric field/quench control of structure and properties of layered perovskite oxides.

关键词： Electrical properties Electroluminescence Magnetic order Magnetic susceptibility Superconductivity

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The Effects of Boron Doping on the Bulk and Surface Acoustic Phonons in Single-Crystal Diamond

arXiv

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arXiv 2022年

作者： Guzman, Erick Kargar, Fariborz Angeles, Frank Meidanshahi, Reza Vatan Grotjohn, Timothy A. Hardy, Aaron Muehle, Matthias Wilson, Richard B. Goodnik, Stephen Balandin, Alexander A. Nano-Device Laboratory Phonon Optimized Engineered Materials Center Department of Electrical and Computer Engineering University of California RiversideCA92521 United States Department of Mechanical Engineering Materials Science and Engineering Program University of California RiversideCA92521 United States School of Electrical Computer and Energy Engineering Arizona State University TempeAZ85281 United States Department of Electrical and Computer Engineering Michigan State University East LansingMI48824 United States Fraunhofer USA Center Midwest East LansingMI48824 United States

We report the results of the investigation of bulk and surface acoustic phonons in the undoped and boron-doped single-crystal diamond films using the Brillouin-Mandelstam light scattering spectroscopy. The evolution of the optical phonons in the same set of samples was monitored with Raman spectroscopy. It was found that the frequency and the group velocity of acoustic phonons decrease non-monotonically with the increasing boron doping concentration, revealing pronounced phonon softening. The change in the velocity of the shear horizontal and the high-frequency pseudo-longitudinal acoustic phonons in the degenerately doped diamond, as compared to the undoped diamond, was as large as ~ 15% and ~12%, respectively. As a result of boron doping, the velocity of the bulk longitudinal and transverse acoustic phonons decreased correspondingly. The frequency of the optical phonons was unaffected at low boron concentration but experienced a strong decrease at the high doping level. The density-functional-theory calculations of the phonon band structure for the pristine and highly-doped sample confirm the phonon softening as a result of boron doping in diamond. The obtained results have important implications for thermal transport in heavily doped diamond, which is a promising material for ultra-wide-band-gap electronics. Copyright © 2022, The Authors. All rights reserved.

关键词： Density functional theory

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Controllable directional excitation and emission of nanoemitters by a subwavelength mie antenna

Controllable directional excitation and emission of nanoemit...

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2020 Frontiers in Optics Conference, FiO 2020

作者： Fang, Jie Wang, Mingsong Yao, Kan Zheng, Yuebing Materials Science and Engineering Program Texas Materials Institute The University of Texas at Austin AustinTX78712 United States Walker Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States

ISBN: (纸本)9781943580804

We derive a universal multipolar model for dipole-sphere hybrids, introduce single subwavelength silicon nanospheres at visible wavelengths with facile size control, and demonstrate controllable directional excitation and emission of nanoemitters (e.g. WS2, MoS2) for on-demand emission property modulations. © OSA 2020 © 2020 The Author(s)

关键词： Nanospheres

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Enhanced Thrombolytic Effect Induced by Acoustic Cavitation Generated from Nitrogen-Doped Annealed Nanodiamond Particles

SSRN

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SSRN 2023年

作者： Zhang, Qi Xue, Honghui Zhang, Haijun Chen, Yuqi Liu, Zijun Fan, Zheng Guo, Xiasheng Wu, Xiaoge Zhang, Dong Tu, Juan Department of Physics Collaborative Innovation Center of Advanced Microstructure Nanjing University Nanjing210093 China Wuxi Vocational Institute of Commerce Jiangsu Wuxi214153 China Shanghai Tenth People's Hospital School of Medicine Tongji University Shanghai200092 China National United Engineering Laboratory for Biomedical Material Modification Branden Industrial Park Shandong Dezhou251100 China School of Mechanical and Aerospace Engineering Nanyang Technological University Singapore639798 Singapore Environment Science and Engineering College Yangzhou University Jiangsu Yangzhou225009 China

In biomedical research, ultrasonic cavitation, especially inertial cavitation (IC) has attracted extensive attentions due to its ability to induce mechanical, chemical and thermal effects. Like ultrasound contrast agent (UCA) microbubbles or droplets, acoustic cavitation can be effectively triggered beyond a certain pressure threshold through the interaction between ultrasound and nucleation particles, leading to an enhanced thrombolytic effect. As a newly developed nanocarbon material, nitrogen-doped annealed nanodiamond (N-AND) has shown promising catalytic performance. To further explore its effects on ultrasonic cavitation, N-AND was synthesized at the temperature of 1000℃. After systematic material characterization, the potential of N-AND to induce enhanced IC activity was assessed for the first time by using passive cavitation detection (PCD). Based on experiments performed at varied material suspension concentration and cycle number, N-AND demonstrated a strong capability to generate significant cavitation characteristics, indicating the formation of stable bubbles from the surface of the materials. Furthermore, N-AND was applied in the in vitro thrombolysis experiments to verify its contribution to ultrasound thrombolysis. The influence of surface hydrophobicity on the cavitation potentials of ND and N-AND was innovatively discussed in combination with the theory of mote-induced nucleation. It is found that the cavitation stability of N-AND was better than that of the commercial UCA microbubbles. This study would provide better understanding of the potential of novel carbonous nanomaterials as cavitation nuclei and is expected to provide guidance for their future biomedical and industrial applications. © 2023, The Authors. All rights reserved.

关键词： Nucleation

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Experimental Validation of a Safe Controller Integration Scheme for Connected Automated Trucks

arXiv

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arXiv 2022年

作者： Alan, Anil He, Chaozhe R. Molnar, Tamas G. Mathew, Johaan C. Bell, A. Harvey Orosz, Gábor The Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States Plus.ai Inc. Santa ClaraCA95014 United States The Department of Mechanical and Civil Engineering California Institute of Technology PasadenaCA91125 United States Visteon Corporation Van Buren Township MI48111 United States Multidisciplinary Design Program University of Michigan Ann ArborMI48109 United States The Department of Civil and Environmental Engineering University of Michigan Ann ArborMI48109 United States

Accomplishing safe and efficient driving is one of the predominant challenges in the controller design of connected automated vehicles (CAVs). It is often more convenient to address these goals separately and integrate the resulting controllers. In this study, we propose a controller integration scheme to fuse performance-based controllers and safety-oriented controllers safely for the longitudinal motion of a CAV. The resulting structure is compatible with a large class of controllers, and offers flexibility to design each controller individually without affecting the performance of the others. We implement the proposed safe integration scheme on a connected automated truck using an optimal-in-energy controller and a safety-oriented connected cruise controller. We validate the premise of the safe integration through experiments with a full-scale truck in two scenarios: a controlled experiment on a test track and a real-world experiment on a public highway. In both scenarios, we achieve energy efficient driving without violating safety. Copyright © 2022, The Authors. All rights reserved.

关键词： Controllers

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Assessing the aneurysm occlusion efficacy of a shear-thinning biomaterial in a 3D-printed model

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Journal of the mechanical Behavior of biomedical Materials 2022年第0期130卷 105156页

作者： Schroeder, Grant Edalati, Masoud Tom, Gregory Kuntjoro, Nicole Gutin, Mark Gurian, Melvin Cuniberto, Edoardo Hirth, Elisabeth Martiri, Alessia Sposato, Maria Teresa Aminzadeh, Selda Eichenbaum, James Alizadeh, Parvin Baidya, Avijit Haghniaz, Reihaneh Nasiri, Rohollah Kaneko, Naoki Mansouri, Abraham Khademhosseini, Ali Sheikhi, Amir Department of Bioengineering University of California Los Angeles 410 Westwood Plaza Los AngelesCA90095 United States University of California Los Angeles 570 Westwood Plaza Los AngelesCA90095 United States David Geffen School of Medicine at UCLA Los AngelesCA United States Department of Mechanical Engineering Rowan University Rowan Hall 201 Mullica Hill Rd GlassboroNJ08028 United States Biomaterials Innovation Research Center Division of Biomedical Engineering Department of Medicine Brigham and Women's Hospital Harvard Medical School CambridgeMA02139 United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA02139 United States Department of Materials Science & Engineering Faculty of Engineering & Technology Tarbiat Modares University Tehran Iran Los AngelesCA90024 United States Department of Radiological Sciences David Geffen School of Medicine University of California Los Angeles 10833 Le Conte Ave Los AngelesCA90095 United States Department of Mechanical Engineering Higher College of Technology Dubai15825 United Arab Emirates Department of Chemical Engineering The Pennsylvania State University University Park PA16802 United States Department of Biomedical Engineering The Pennsylvania State University University Park PA16802 United States

Metallic coil embolization is a common method for the endovascular treatment of visceral artery aneurysms (VAA) and visceral artery pseudoaneurysms (VAPA);however, this treatment is suboptimal due to the high cost of coils, incomplete volume occlusion, poor reendothelialization, aneurysm puncture, and coil migration. Several alternative treatment strategies are available, including stent flow diverters, glue embolics, gelfoam slurries, and vascular mesh plugs—each of which have their own disadvantages. Here, we investigated the in vitro capability of a shear-thinning biomaterial (STB), a nanocomposite hydrogel composed of gelatin and silicate nanoplatelets, for the minimally-invasive occlusion of simple necked aneurysm models. We demonstrated the injectability of STB through various clinical catheters, engineered an in vitro testing apparatus to independently manipulate aneurysm neck diameter, fluid flow rate, and flow waveform, and tested the stability of STB within the models under various conditions. Our experiments show that STB is able to withstand at least 1.89 Pa of wall shear stress, as estimated by computational fluid dynamics. STB is also able to withstand up to 10 mL s−1 pulsatile flow with a waveform mimicking blood flow in the human femoral artery and tolerate greater pressure changes than those in the human aorta. We ultimately found that our in vitro system was limited by supraphysiologic pressure changes caused by aneurysm models with low compliance. © 2022 Elsevier Ltd

关键词： Shear thinning

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