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Attenuation coefficient estimation for PET/MRI with Bayesian deep learning pseudo-CT and maximum likelihood estimation of activity and attenuation

arXiv

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arXiv 2020年

作者： Leynes, Andrew Palmera Ahn, Sangtae P. Wangerin, Kristen A. Kaushik, Sandeep S. Wiesinger, Florian Hope, Thomas A. Larson, Peder E.Z. The Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States The UC Berkeley Joint Graduate Program in Bioengineering BerkeleyCA United States UC San Francisco Joint Graduate Program in Bioengineering San FranciscoCA United States GE Research NiskayunaNY United States GE Healthcare WaukeshaWI United States GE Healthcare Munich Germany The Department of Computer Science Technical University of Munich Munich Germany The Department of Radiology San Francisco VA Medical Center San FranciscoCA United States

A major remaining challenge for magnetic resonance-based attenuation correction methods (MRAC) is their susceptibility to sources of MRI artifacts (e.g. implants, motion) and uncertainties due to the limitations of MRI contrast (e.g. accurate bone delineation and density, and separation of air/bone). We propose using a Bayesian deep convolutional neural network that, in addition to generating an initial pseudo-CT from MR data, also produces uncertainty estimates of the pseudo-CT to quantify the limitations of the MR data. These outputs are combined with MLAA reconstruction that uses the PET emission data to improve the attenuation maps. With the proposed approach (UpCT-MLAA), we demonstrate accurate estimation of PET uptake in pelvic lesions and show recovery of metal implants. In patients without implants, UpCT-MLAA had acceptable but slightly higher RMSE than Zero-echo-time and Dixon Deep pseudo-CT when compared to CTAC. In patients with metal implants, MLAA recovered the metal implant;however, anatomy outside the implant region was obscured by noise and crosstalk artifacts. Attenuation coefficients from the pseudo-CT from Dixon MRI were accurate in normal anatomy;however, the metal implant region was estimated to have attenuation coefficients of air. UpCT-MLAA estimated attenuation coefficients of metal implants alongside accurate anatomic depiction outside of implant regions. © 2020, CC BY.

关键词： Magnetic resonance

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Clinical text generation through leveraging medical concept and relations

arXiv

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arXiv 2019年

作者： Lee, Wangjin Park, Hyeryun Yoon, Jooyoung Kim, Kyeongmo Choi, Jinwook Interdisciplinary Program in Bioengineering Graduate School Seoul National University Department of Biomedical Engineering College of Medicine Seoul National University

With a neural sequence generation model, this study aims to develop a method of writing the patient clinical texts given a brief medical history. As a proof-of-a-concept, we have demonstrated that it can be workable to use medical concept embedding in clinical text generation. Our model was based on the Sequence-to-Sequence architecture and trained with a large set of de-identified clinical text data. The quantitative result shows that our concept embedding method decreased the perplexity of the baseline architecture. Also, we discuss the analyzed results from a human evaluation performed by medical doctors. Copyright © 2019, The Authors. All rights reserved.

关键词： Embeddings

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A metabolite specific 3D stack-of-spiral bSSFP sequence for improved lactate imaging in hyperpolarized [1-13C]pyruvate studies on a 3T clinical scanner

arXiv

引用

arXiv 2020年

作者： Tang, Shuyu Bok, Robert Qin, Hecong Reed, Galen VanCriekinge, Mark Santos, Romelyn Delos Overall, William Santos, Juan Gordon, Jeremy Wang, Zhen Jane Vigneron, Daniel B. Larson, Peder E.Z. UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco University of California Berkeley United States Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States HeartVista Los AltosCA United States

Purpose: The balanced steady-state free precession sequence has been previously explored to improve the efficient use of non-recoverable hyperpolarized 13C magnetization, but suffers from poor spectral selectivity and long acquisition time. The purpose of this study was to develop a novel metabolite-specific 3D bSSFP ("MS-3DSSFP") sequence with stack-of-spiral readouts for improved lactate imaging in hyperpolarized [1-13C]pyruvate studies on a clinical 3T scanner. Methods: Simulations were performed to evaluate the spectral response of the MS-3DSSFP sequence. Thermal 13C phantom experiments were performed to validate the MS-3DSSFP sequence. In vivo hyperpolarized [1-13C]pyruvate studies were performed to compare the MS-3DSSFP sequence with metabolite specific gradient echo ("MS-GRE") sequences for lactate imaging. Results: Simulations, phantom and in vivo studies demonstrate that the MS-3DSSFP sequence achieved spectrally selective excitation on lactate while minimally perturbing other metabolites. Compared with MS-GRE sequences, the MS-3DSSFP sequence showed approximately a 2.5-fold SNR improvement for lactate imaging in rat kidneys, prostate tumors in a mouse model and human kidneys. Conclusions: Improved lactate imaging using the MS-3DSSFP sequence in hyperpolarized [1-13C]pyruvate studies was demonstrated in animals and humans. The MS-3DSSFP sequence could be applied for other clinical applications such as in the brain or adapted for imaging other metabolites such as pyruvate and bicarbonate. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Assessment of circulating extracellular vesicles from calorie-restricted mice and humans in ischaemic injury models

Journal of Extracellular Biology

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Journal of Extracellular Biology 2023年第5期2卷 e86页

作者： Jaimes, Manuel S. V. Liao, Chia-Te Chen, Max M. Czosseck, Andreas Lee, Tsung-Lin Chou, Yu-Hsiang Chen, Yung-Ming Lin, Shuei-Liong Lai, James J. Lundy, David J. Graduate Institute of Biomedical Materials & Tissue Engineering Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei Taiwan Division of Nephrology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan TMU Research Center of Urology and Kidney (TMU-RCUK) Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine National Taiwan University Hospital College of Medicine National Taiwan University Taipei Taiwan Graduate Institute of Physiology College of Medicine National Taiwan University Taipei Taiwan Department of Bioengineering University of Washington Seattle WA United States Department of Materials Science and Engineering National Taiwan University of Science and Technology Taipei Taiwan International PhD Program in Biomedical Engineering Taipei Medical University Taipei Taiwan Center for Cell Therapy Taipei Medical University Hospital Taipei Taiwan

Calorie restriction (CR) and fasting affect lifespan, disease susceptibility and response to acute injury across multiple animal models, including ischaemic injuries such as myocardial infarction or kidney hypoxia. The cargo and function of circulating extracellular vesicles (EV) respond to changes in host physiology, including exercise, injury, and other interventions. Thus, we hypothesised that EVs induced following CR may reflect some of the beneficial properties of CR itself. In a pilot study, EVs were isolated from mice following 21 days of 30 % CR, and from eight human donors after 72 h water-only fasting. EV size, concentration and morphology were profiled by NTA, western blot and cryoEM, and their function was assessed using multiple assays related to ischaemic diseases. We found that EVs from post-fasting samples better protected cardiac cells from hypoxia/reperfusion (H/R) injury compared to pre-fasting EVs. However, there was no difference when used to treat H/R-injured kidney epithelial cells. Post-fasting derived EVs slowed the rate of fibroblast migration and slightly reduced macrophage inflammatory gene expression compared to pre-fasting derived EVs. Lastly, we compared miRNA cargos of pre- and post-fasting human serum EVs and found significant changes in a small number of miRNAs. We conclude that fasting appears to influence EV cargo and function, with varied effects worthy of further exploration. © 2023 The Authors. Journal of Extracellular Biology published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles.

关键词： calorie restriction cardiomyocyte diet extracellular vesicle fasting hypoxia ketone macrophage microRNA serum

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Dissecting and rebuilding the glioblastoma microenvironment with engineered materials (vol 4, pg 651, 2019)

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NATURE REVIEWS MATERIALS 2020年第10期5卷 780-780页

作者： Wolf, Kayla J. Chen, Joseph Coombes, Jason D. Aghi, Manish K. Kumar, Sanjay University of California Berkeley–University of California San Francisco Graduate Program in Bioengineering Berkeley USA Department of Bioengineering University of California Berkeley Berkeley USA Department of Inflammation Biology Faculty of Life Sciences and Medicine King’s College London London UK Department of Neurosurgery University of California San Francisco (UCSF) San Francisco USA Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley USA

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Corrigendum to "Mathematical model of modified hybrid pump mechanism for cardiopulmonary resuscitation" [Computer methods and programs in biomedicine 206 (2021) 106106]

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Computer methods and programs in biomedicine 2022年 218卷 106711页

作者： Dong Ah Shin Jung Chan Lee Interdisciplinary Program in Bioengineering Graduate School Seoul National University Seoul 08826 Republic of Korea. Department of Biomedical Engineering College of Medicine and Institute of Medical and Biological Engineering Medical Research Center Seoul National University Seoul 03080 Republic of Korea Institute of BioEngineering Bio-MAX Institute Seoul National University Seoul 08826 Republic of Korea. Electronic address: ljch@snu.ac.kr.

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A Regional bolus tracking and Real-time B1 Calibration method for Hyperpolarized 13C MRI

arXiv

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arXiv 2020年

作者： Tang, Shuyu Milshteyn, Eugene Reed, Galen Gordon, Jeremy Bok, Robert Zhu, Xucheng Zhu, Zihan Vigneron, Daniel B. Larson, Peder E.Z. UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco United States University of California Berkeley United States Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States HeartVista Los AltosCA United States

Purpose: Acquisition timing and B1 calibration are two key factors that affect the quality and accuracy of hyperpolarized 13C MRI. The goal of this project was to develop a new approach using regional bolus tracking to trigger Bloch-Siegert B1 mapping and real-time B1 calibration based on regional B1 measurements, followed by dynamic imaging of hyperpolarized 13C metabolites in ***: The proposed approach was implemented on a system which allows real-time data processing and real-time control on the sequence. Real-time center frequency calibration upon the bolus arrival was also added. The feasibility of applying the proposed framework for in vivo hyperpolarized 13C imaging was tested on healthy rats, tumor-bearing mice and a healthy volunteer on a clinical 3T scanner following hyperpolarized [1-13C]pyruvate injection. Multichannel receive coils were used in the human ***: Automatic acquisition timing based on either regional bolus peak or bolus arrival was achieved with the proposed framework. Reduced blurring artifacts in real-time reconstructed images were observed with real-time center frequency calibration. Real-time computed B1 scaling factors agreed with real-time acquired B1 maps. Flip angle correction using B1 maps results in a more consistent quantification of metabolic activity (i.e, pyruvate-to-lactate conversion, kPL). Experiment recordings are provided to demonstrate the real-time actions during the ***: The proposed method was successfully demonstrated on animals and a human volunteer, and is anticipated to improve the efficient use of the hyperpolarized signal as well as the accuracy and robustness of hyperpolarized 13C imaging. Copyright © 2020, The Authors. All rights reserved.

关键词： Mapping

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Customized nanoparticle probes for biomedical imaging, diagnostics and therapeutics applications 11

Customized nanoparticle probes for biomedical imaging, diagn...

引用

11th Annual TechConnect World Innovation Conference and Expo, Held Jointly with the 20th Annual Nanotech Conference and Expo,the 2018 SBIR/STTR Spring Innovation Conference, and the Defense TechConnect DTC Spring Conference

作者： Nallathamby, Prakash D. Roeder, Ryan K. Bioengineering Graduate Program-AME University of Notre Dame Notre DameIN United States Notre DameIN United States

ISBN: (纸本)9780998878249

The modular synthetic approach that was developed to design a spectral library of core-shell nanoparticle contrast agents, which will have broad applications in biomedical imaging due to the potential for multi-modal imaging (e.g., fluorescence, MRI, X-ray) and active targeting through molecular surface functionalization. Gadolinium oxide, hafnium oxide, and gold core compositions were prepared at a common size (12-15 nm) using sol-gel and microemulsion syntheses. Nanoparticle cores were encapsulated in a silica shell with a controlled thickness of 1-15 nm using polymer shells or microemulsions. Controlled silica shell formation enabled the incorporation of fluorescent molecules and provided a common platform for molecular surface functionalization using silane chemistry. Antibodies and other small molecules were efficiently conjugated to the nanoparticles using carbodiimide chemistry. We anticipate that this modular approach will provide a platform for facile customization of multi-component nanoparticles with tailored surface functionality that will have applications beyond the biomedical field due to the ability to customize electromagnetic properties in size, shape, and elemental composition-dependent manner. © 2018 OOSV. All rights reserved.

关键词： Silica

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Author Correction: A high-performance neuroprosthesis for speech decoding and avatar control

引用

Nature 2024年第8021期631卷 E13页

作者： Sean L Metzger Kaylo T Littlejohn Alexander B Silva David A Moses Margaret P Seaton Ran Wang Maximilian E Dougherty Jessie R Liu Peter Wu Michael A Berger Inga Zhuravleva Adelyn Tu-Chan Karunesh Ganguly Gopala K Anumanchipalli Edward F Chang Department of Neurological Surgery University of California San Francisco San Francisco CA USA. Weill Institute for Neuroscience University of California San Francisco San Francisco CA USA. University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering Berkeley CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Speech Graphics Ltd Edinburgh UK. Department of Neurology University of California San Francisco San Francisco CA USA. Department of Neurological Surgery University of California San Francisco San Francisco CA USA. edward.chang@ucsf.edu. Weill Institute for Neuroscience University of California San Francisco San Francisco CA USA. edward.chang@ucsf.edu. University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering Berkeley CA USA. edward.chang@ucsf.edu.

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Go with the FLOW: Visualizing spatiotemporal dynamics in optical widefield calcium imaging

arXiv

引用

arXiv 2020年

作者： Linden, Nathaniel J. Tabuena, Dennis R. Steinmetz, Nicholas A. Moody, William J. Brunton, Steven L. Brunton, Bingni W. Department of Bioengineering University of Washington Seattle United States Department of Biology University of Washington Seattle United States Graduate Program in Neuroscience University of Washington Seattle United States Department of Biological Structure University of Washington Seattle United States Department of Mechanical Engineering University of Washington Seattle United States

Widefield calcium imaging has recently emerged as a powerful experimental technique to record coordinated large-scale brain activity. These measurements present a unique opportunity to characterize spatiotemporally coherent structures that underlie neural activity across many regions of the brain. In this work, we leverage analytic techniques from fluid dynamics to develop a visualization framework that highlights features of flow across the cortex, mapping wave fronts that may be correlated with behavioral events. First, we transform the time series of widefield calcium images into time-varying vector fields using optic flow. Next, we extract concise diagrams summarizing the dynamics, which we refer to as FLOW (flow lines in optical widefield imaging) portraits. These FLOW portraits provide an intuitive map of dynamic calcium activity, including regions of initiation and termination, as well as the direction and extent of activity spread. To extract these structures, we use the finite-time Lyapunov exponent (FTLE) technique developed to analyze time-varying manifolds in unsteady fluids. Importantly, our approach captures coherent structures that are poorly represented by traditional modal decomposition techniques. We demonstrate the application of FLOW portraits on three simple synthetic datasets and two widefield calcium imaging datasets, including cortical waves in the developing mouse and spontaneous cortical activity in an adult mouse. © 2020, CC BY.

关键词： Brain

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