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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

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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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Spectral DiffuserCam: lensless snapshot hyperspectral imaging with a spectral filter array

arXiv

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arXiv 2020年

作者： Monakhova, Kristina Yanny, Kyrollos Aggarwal, Neerja Waller, Laura Department of Electrical Engineering & Computer Sciences University of California BerkeleyCA94720 United States UCB/UCSF Joint Graduate Program in Bioengineering University of California BerkeleyCA94720 United States

Hyperspectral imaging is useful for applications ranging from medical diagnostics to crop monitoring;however, traditional scanning hyperspectral imagers are prohibitively slow and expensive for widespread adoption. Snapshot techniques exist but are often confined to bulky bench-top setups or have low spatio-spectral resolution. In this paper, we propose a novel, compact, and inexpensive computational camera for snapshot hyperspectral imaging. Our system consists of a repeated spectral filter array placed directly on the image sensor and a diffuser placed close to the sensor. Each point in the world maps to a unique pseudorandom pattern on the spectral filter array, which encodes multiplexed spatio-spectral information. A sparsity-constrained inverse problem solver then recovers the hyperspectral volume with good spatio-spectral resolution. By using a spectral filter array, our hyperspectral imaging framework is flexible and can be designed with contiguous or non-contiguous spectral filters that can be chosen for a given application. We provide theory for system design, demonstrate a prototype device, and present experimental results with high spatio-spectral resolution. © 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement Copyright © 2020, The Authors. All rights reserved.

关键词： Spectroscopy

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Resistive-pulse sensing tumor-derived exosome detection device 22

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

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22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018

作者： Carey, Thomas R. Yu, Connie W. Hall, Jennifer Sohn, Lydia L. UC Berkeley UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States UC Berkeley Molecular and Cell Biology United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9781510897571

We present the theory, design, and proof-of-concept demonstration of a tumor-derived exosome detection platform that enables non-invasive, cost-effective, point-of-care cancer screening. Our platform detects exosomes displaying a specific surface antigen by electronically measuring through node-pore sensing the effective size increase that occurs when exosomes bind to colloids functionalized with specific antibodies. We have demonstrated that our platform can differentially detect exosomes derived from A549 cells (a non-small cell lung cancer cell line) and BEAS-2B cells (a non-malignant bronchial epithelial cell line). Copyright © (2018) by Chemical and Biological Microsystems Society. All rights reserved.

关键词： Tumors

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

arXiv

引用

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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Tissue Tension Permits Β-Catenin Phosphorylation to Drive Mesoderm Specification in Human Embryonic Stem Cells

SSRN

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SSRN 2023年

作者： Ayad, Nadia M.E. Lakins, Johnathon N. Ghagre, Ajinkya Ehrlicher, Allen J. Weaver, Valerie M. Graduate Program in Bioengineering University of California San Francisco University of California Berkeley San FranciscoCA94143 United States Center for Bioengineering and Tissue Regeneration Department of Surgery University of California San Francisco San FranciscoCA94143 United States Department of Bioengineering McGill University MontrealQCH3A 0E9 Canada Department of Bioengineering Department of Anatomy and Cell Biology Department of Biomedical Engineering Department of Mechanical Engineering Centre for Structural Biology Rosalind and Morris Goodman Cancer Institute McGill University MontrealQCH3A 1A3 Canada Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California San Francisco San FranciscoCA94143 United States UCSF Comprehensive Cancer Center Helen Diller Family Cancer Research Center University of California San Francisco San FranciscoCA94143 United States Department of Bioengineering and Therapeutic Sciences Department of Radiation Oncology University of California San Francisco San FranciscoCA94143 United States

The role of morphogenetic forces in cell fate specification is an area of intense interest. Our prior studies suggested that the development of high cell-cell tension in human embryonic stem cells (hESC) colonies permits the Src-mediated phosphorylation of junctional β-catenin that accelerates its release to potentiate Wnt-dependent signaling critical for initiating mesoderm specification. Using an ectopically expressed nonphosphorylatable mutant of β-catenin (Y654F), we now provide direct evidence that impeding tension-dependent Src-mediated β-catenin phosphorylation impedes the expression of Brachyury (T) and the epithelial-to-mesenchymal transition (EMT) necessary for mesoderm specification. Addition of exogenous Wnt3a or inhibiting GSK3β activity rescued mesoderm expression, emphasizing the importance of force dependent Wnt signaling in regulating mechanomorphogenesis. Our work provides a framework for understanding tension-dependent β-catenin/Wnt signaling in the self-organization of tissues during developmental processes including gastrulation. © 2023, The Authors. All rights reserved.

关键词： Tissue

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

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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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Author Correction: Multi-institutional atlas of brain metastases informs spatial modeling for precision imaging and personalized therapy

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Nature communications 2025年第1期16卷 5096页

作者： Jorge Barrios Evan Porter Dante P I Capaldi Taman Upadhaya William C Chen Julian R Perks Aditya Apte Michalis Aristophanous Eve LoCastro Dylan Hsu Payton H Stone Javier E Villanueva-Meyer Gilmer Valdes Fei Jiang Michael Maddalena Ase Ballangrud Kayla Prezelski Hui Lin Jinger Y Sun Muhtada A K Aldin Oi Wai Chau Benjamin Ziemer Maasa Seaberg Penny K Sneed Jean L Nakamura Lauren C Boreta Shannon E Fogh David R Raleigh Jessica Chew Harish Vasudevan Soonmee Cha Christopher Hess Ruben Fragoso David B Shultz Luke Pike Shawn L Hervey-Jumper Derek S Tsang Philip Theodosopoulos Daniel Cooke Stanley H Benedict Ke Sheng Jan Seuntjens Catherine Coolens Joseph O Deasy Steve Braunstein Olivier Morin Department of Radiation Oncology University of California San Francisco San Francisco CA USA. Department of Radiation Oncology University of California Davis Health Sacramento CA USA. Department of Radiation Oncology Memorial Sloan Kettering New York NY USA. Department of Medical Physics Memorial Sloan Kettering New York NY USA. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco CA USA. Department of Neurological Surgery University of California San Francisco San Francisco CA USA. Department of Epidemiology and Biostatistics University of California San Francisco San Francisco CA USA. Moffit Cancer Center Tampa Florida USA. Radiation Medicine Program Princess Margaret Cancer Centre University Health Network Toronto ON Canada. Department of Medical Biophysics University of Toronto Toronto ON Canada. UCSF/UC Berkeley Graduate Program in Bioengineering San Francisco CA USA. Department of Pathology University of California San Francisco San Francisco CA USA. Department of Radiation Oncology University of California San Francisco San Francisco CA USA. Olivier.Morin@ucsf.edu. UCSF/UC Berkeley Graduate Program in Bioengineering San Francisco CA USA. Olivier.Morin@ucsf.edu.

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Author Correction: Autophagy restricts Mycobacterium tuberculosis during acute infection in mice

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Nature microbiology 2024年第7期9卷 1899页

作者： Guillaume R Golovkine Allison W Roberts Huntly M Morrison Rafael Rivera-Lugo Rita M McCall Hannah Nilsson Nicholas E Garelis Teresa Repasy Michael Cronce Jonathan Budzik Erik Van Dis Lauren M Popov Gabriel Mitchell Reena Zalpuri Danielle Jorgens Jeffery S Cox Department of Molecular and Cell Biology University of California Berkeley CA USA. Evotec Toulouse France. Department of Plant & Microbial Biology University of California Berkeley CA USA. Bio-Rad Laboratories Seattle WA USA. Department of Bioengineering University of California Berkeley CA USA. UC Berkeley-UCSF Graduate program in Bioengineering Berkeley CA USA. Department of Medicine University of California San Francisco CA USA. Department of Immunology University of Washington School of Medicine Seattle WA USA. Novome Biotechnologies San Francisco CA USA. Open Innovation @ NITD Novartis Institute for Tropical Diseases Emeryville CA USA. Electron Microscope Laboratory University of California Berkeley CA USA. Department of Molecular and Cell Biology University of California Berkeley CA USA. jeff.cox@berkeley.edu.

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Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes

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Scientific Reports 2025年第1期15卷 1-9页

作者： Daniel Foyt Yiming Kuang Klaus Yserentant Bo Huang Samma Rehem UCSF-UC Berkeley Joint Graduate Program in Bioengineering University of California San Francisco San Francisco CA 94143 USA Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA 94143 USA Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94143 USA Chan Zuckerberg Biohub San Francisco San Francisco CA 94158 USA Barnard College of Columbia University New York City NY 10027 USA

We have developed a method along with a Python-based analysis tool to capture images and produce flow-cytometry-like data for adherent cell culture utilizing simple accessible microscopes. Leveraging the recently developed generalist algorithms for cell segmentation, our approach efficiently quantifies single-cell fluorescence signals. We demonstrated the utility of this method by screening a set of 88 prime editing conditions using the integration of mNeonGreen211as a reporter.

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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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