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Three-Dimensional Endothelium-Lined Microfabricated Channels as in Vitro assays for Sickle Cell Vaso-Occlusion

Blood 2008年第11期112卷 4790-4790页

作者： Michelle Tsai Thomas P. Hunt Daniel A. Fletcher Wilbur Aaron Lam Bioengineering UC Berkeley Berkeley CA USA Bioengineering Biophysics Graduate Group UC Berkeley Berkeley CA USA Pediatrics Bioengineering UCSF UC Berkeley Berkeley CA USA

Vaso-occlusion in sickle cell disease is fundamentally biophysical in nature, involving a complex set of cellular interactions. Originally attributed solely to the entrapment of abnormally rigid sickle red cells (RBCs) in the microcirculation, this process is now known to involve the decreased deformability of white blood cells (WBCs) and increased endothelial adhesion to different cell types (sickle RBCs, reticulocytes, WBCs, platelets). These biophysical interactions, which are also mediated biochemically by a variety of soluble factors (coagulation proteins, inflammatory mediators, reactive oxygen species, free hemoglobin, etc.), then ultimately lead to microvascular obstruction. However, in vitro experimental approaches that measure the vaso-occlusive properties of sickle blood cells have been unable to separate the contributions of decreased cell deformability and cell-cell adhesion in a single assay. Historically, cell deformability is measured using techniques such as micropipette aspiration, micropore filtration, and ektacytometry, whereas adhesive interactions between the endothelium, blood cells, and soluble factors are assessed using endothelial-lined flow chamber assays. No existing technique effectively evaluates both cell deformability and cell adhesion simultaneously, which is required to comprehensively study sickle cell vaso-occlusion. In the current study, we present an “endothelialized” microfluidic system that simultaneously integrates cell deformability and cell adhesion under physiologic microvascular flow conditions to investigate the underlying biophysical mechanisms of sickle cell vaso-occlusion. Briefly, a layer of human umbilical vein endothelial cells (HUVECs) was cultured along the inner walls of microfabricated microchannels made of the biocompatible and optically transparent polymer polydimethylsiloxane, or PDMS (Figure). Standard lab-on-chip photolithography techniques were utilized to design and create the microchannels, which geomet

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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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A compact planar triple-nuclear coil for small animal 1H, 13C, and 31P Metabolic MR Imaging at 14.1 T

arXiv

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arXiv 2021年

作者： Leynes, A.P. Chen, Y. Sukumar, S. Xu, D. Zhang, X. Department of Radiology and Biomedical Imaging University of California San Francisco Byers Hall 102D 1700 4th Street San FranciscoCA94158 United States UC Berkeley and UCSF Joint Graduate Group in Bioengineering San Francisco BerkeleyCA United States

Multi-nuclear radio-frequency (RF) coils at ultrahigh field strengths are challenging to develop due to the high operating frequency, increased electromagnetic interaction among the coil elements, and increased electromagnetic interaction between the coils and the subject. In this work, a triple-nuclear surface coil for 1H, 13C, and 31P for small animal metabolic imaging at 14.1 T is built by nesting three surface coil geometries: a lumped-element L-C loop coil, a butterfly coil, and a microstrip transmission line (MTL) resonator. The loop coil, butterfly coil, and MTL are tuned to 31P, 13C, and 1H, respectively. The successful bench tests and phantom imaging with this novel triple-nuclear coil demonstrates the feasibility of the design for triple-nuclear MR imaging and spectroscopy studies at the ultrahigh field of 14.1 T. In particular, the microstrip transmission line resonator demonstrates excellent coil performance for proton imaging at 600 MHz, where conventional lumped-element design is limited. © 2021, CC BY.

关键词： Resonators

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Imaging neurotransmitter transport in live cells with stimulated Raman scattering microscopy

arXiv

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arXiv 2022年

作者： Manifold, Bryce Dorlhiac, Gabriel F. Landry, Markita P. Streets, Aaron Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Biophysics Graduate Group University of California Berkeley BerkeleyCA94720 United States Department of Chemical and Biomolecular Engineering University of California Berkeley BerkeleyCA94720 United States Innovative Genomics Institute University of California Berkeley BerkeleyCA94720 United States California Institute for Quantitative Biosciences QB3 University of California Berkeley BerkeleyCA94720 United States Chan-Zuckerberg Biohub San FranciscoCA94158 United States UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California Berkeley BerkeleyCA94720 United States

Chemical neurotransmission is central to neurotypical brain function but also implicated in a variety of psychiatric and neurodegenerative diseases. The release dynamics of neurotransmitters is correlated with but distinct from neuronal electrical signal propagation. It is therefore necessary to track neurotransmitter modulation separately from neuron electrical activity. Here, we present a new approach for imaging deuterated neurotransmitter molecules in the cell-silent window with stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we perform direct imaging of deuterated dopamine and GABA in PC12 chromaffin cells, and in primary hippocampal neurons, respectively, based on the carbon-deuterium vibrational frequencies. We demonstrate that SRS imaging of these isotopologues directly visualizes intracellular neurotransmitters without changing the neurotransmitters’ chemical identity, and requiring custom synthesis or genetic encoding protocols. We further show that stimulation of neurotransmitter release results in an overall 20-50% intracellular neurotransmitter signal reduction in agreement with comparable neurotransmission dynamics studies, with the ability to observe inter- and intracellular variation in vesicular neurotransmitter release. Taken together, our data suggest that neurotransmitter isotopologues can serve as a commercially-available, biocompatible, and generalizable method to image neurotransmitters with deuterated molecules that are virtually chemically identical to their native counterparts. © 2022, CC BY.

关键词： Stimulated Raman scattering

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Performance Evaluation and Comparison of two Triple-nuclear RF Resonators for 1H/19F/31P MR Imaging at 9.4T

Performance Evaluation and Comparison of two Triple-nuclear ...

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IEEE International Conference on Real-time Computing and Robotics (RCAR)

作者： Feng Du Shengping Liu Nan Li Congcong Liu Qiaoyan Chen Shuai Zhang Haifeng Wang Xiaoliang Zhang Ye Li Chongqing University of Technology Chongqing Chongqing China Lauterbur Research Center for Biomedical Imaging Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen Guang Dong China UCSF/UC Berkeley Joint Graduate Group in Bioengineering San Francisco CA USA

ISBN: (数字)9781728137261

ISBN: (纸本)9781728137278

Radio frequency (RF) coils are critical devices in magnetic resonance (MR) systems for transmitting and receiving magnetic resonance signals. However, the required high operating frequency at ultrahigh magnetic fields makes the design of highly efficient radio frequency (RF) transmit or receive coils technically challenging. This is particularly true in the double-tuned or triple-tuned RF coils usually required in heteronuclear MRI and MRS where multiple nuclei, such as 1 H, 19 F, and 31 P, are involved. The performance of RF coils is a critically important factor for realizing the high sensitivity provided by ultrahigh magnetic fields to contribute towards the advancement of a novel human in vivo application at 9.4T. In this work, two different configurations of novel triple-nuclear ( 1 H/ 19 F/ 31 P) RF resonators were proposed for the ultrahigh field 9.4T applications. We also reported on the design and construction, and a field-circuit co-simulation was used to obtain the S-parameters, B 1 + field and specific absorption rate (SAR) distributions to evaluate and compare their performance. And the characteristics and advantages of the proposed two different configurations of triple-nuclear RF resonators in the applications of 1 H/ 19 F/ 31 P at ultrahigh magnetic field were investigated.

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Physics-driven Deep Learning for PET/MRI

arXiv

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arXiv 2022年

作者： Rajagopal, Abhejit Leynes, Andrew P. Dwork, Nicholas Scholey, Jessica E. Hope, Thomas A. Larson, Peder E.Z. Department of Radiology and Biomedical Imaging University of California San Francisco94158 United States Uc Berkeley-UCSF Joint Graduate Program in Bioengineering University of California San Francisco United States University of California BerkeleyCA United States Department of Radiation Oncology University of California San Francisco94158 United States Departments of Pediatrics and Radiology University of Colorado Anschutz 80045 United States

In this paper, we review physics- and data-driven reconstruction techniques for simultaneous positron emission tomography (PET) / magnetic resonance imaging (MRI) systems, which have significant advantages for clinical imaging of cancer, neurological disorders, and heart disease. These reconstruction approaches utilize priors, either structural or statistical, together with a physics-based description of the PET system response. However, due to the nested representation of the forward problem, direct PET/MRI reconstruction is a nonlinear problem. We elucidate how a multi-faceted approach accommodates hybrid data- and physics-driven machine learning for reconstruction of 3D PET/MRI, summarizing important deep learning developments made in the last 5 years to address attenuation correction, scattering, low photon counts, and data consistency. We also describe how applications of these multi-modality approaches extend beyond PET/MRI to improving accuracy in radiation therapy planning. We conclude by discussing opportunities for extending the current state-of-the-art following the latest trends in physics- and deep learning-based computational imaging and next-generation detector hardware. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Ten simple rules for reproducible research in jupyter notebooks

arXiv

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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Simulation of lung alveolar type II epithelial wound healing in vitro

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Journal of Critical Care 2009年第3期24卷 e21-e22页

作者： Sean H.J. Kim C. Anthony Hunt UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California Berkeley Department of Bioengineering and Therapeutic Sciences University of California San Francisco

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Detection of Isoforms Differing by a Single Charge Unit in Individual Cells

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Angewandte Chemie 2016年第40期128卷

作者： Augusto M. Tentori Kevin A. Yamauchi Amy E. Herr The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA Department of Bioengineering UC Berkeley 308B Stanley Hall Berkeley CA 94720 USA

To measure protein isoforms in individual mammalian cells, we report single‐cell resolution isoelectric focusing (scIEF) and high‐selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17‐pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single‐charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.

关键词： Einzelzellanalyse Immunassays Isoelektrische Fokussierung Lab-on-a-Chip Proteomik

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Mechanistic simulations explain paradoxical saquinavir metabolism during in vitro vectorial transport study

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Journal of Critical Care 2009年第3期24卷 e19-e20页

作者： Lam, Tai Ning Hunt, C. Anthony UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California Berkeley Department of Bioengineering and Therapeutic Sciences University of California San Francisco

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