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Author Correction: ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway

Nature chemical biology 2024年 2024 Nov 8页

作者： Jordan J Baker Jie Shi Shangying Wang Elena M Mujica Simone Bianco Sara Capponi John E Dueber Department of Bioengineering University of California Berkeley CA USA. UC Berkeley and UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA USA. NSF Center for Cellular Construction University of California San Francisco CA USA. Department of Functional Genomics and Cellular Engineering IBM Almaden Research Center San Jose CA USA. Bay Area Institute of Science Altos Labs Redwood City CA USA. NSF Center for Cellular Construction University of California San Francisco CA USA. sara.capponi@***. Department of Functional Genomics and Cellular Engineering IBM Almaden Research Center San Jose CA USA. sara.capponi@***. Department of Bioengineering University of California Berkeley CA USA. jdueber@berkeley.edu. NSF Center for Cellular Construction University of California San Francisco CA USA. jdueber@berkeley.edu. Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA. jdueber@berkeley.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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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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Deep learning-guided design of dynamic proteins

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Science (New York, N.Y.) 2025年第6749期388卷 eadr7094页

作者： Amy B Guo Deniz Akpinaroglu Christina A Stephens Michael Grabe Colin A Smith Mark J S Kelly Tanja Kortemme The UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco San Francisco CA USA. Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA USA. Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA USA. Cardiovascular Research Institute University of California San Francisco San Francisco CA USA. Department of Chemistry Wesleyan University Middletown CT USA. Quantitative Biosciences Institute University of California San Francisco San Francisco CA USA. Chan Zuckerberg Biohub San Francisco CA USA.

Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-guided approach for de novo design of dynamic changes between intradomain geometries of proteins, similar to switch mechanisms prevalent in nature, with atomic-level precision. We solve four structures that validate the designed conformations, demonstrate modulation of the conformational landscape by orthosteric ligands and allosteric mutations, and show that physics-based simulations are in agreement with deep-learning predictions and experimental data. Our approach demonstrates that new modes of motion can now be realized through de novo design and provides a framework for constructing biology-inspired, tunable, and controllable protein signaling behavior de novo.

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Synthetic CT Generation Using MRI with Deep Learning: How Does the Selection of Input Images Affect the Resulting Synthetic CT?

Synthetic CT Generation Using MRI with Deep Learning: How Do...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Andrew P. Leynes Peder E. Z. Larson UC Berkeley - UC San Francisco Joint Graduate Program in Bioengineering

ISBN: (纸本)9781538646595

Synthetic x-ray computed tomography (CT) images derived from magnetic resonance imaging (MRI) is a recent area of focus for medical imaging researchers for applications in attenuation correction in simultaneous PET/MRI systems and MRI-guided radiotherapy planning. Several research groups have demonstrated the potential of deep learning to generate the synthetic CT images, however, there are several major open questions that remain with this approach. We investigated how the selection of MRI inputs affect the resulting output using a fixed network. We found that Dixon MRI may be sufficient for quantitatively accurate synthetic CT images and ZTE MRI may provide additional information to capture bowel air distributions.

关键词： synthetic ct deep learning mri Dixon mri zero echo-time mri

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Performance evaluation and comparison of two triple-nuclear RF resonators for 1H/19F/31PMR imaging at 9.4T

Performance evaluation and comparison of two triple-nuclear ...

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2019 IEEE International Conference on Real-Time Computing and Robotics, RCAR 2019

作者： Du, Feng Liu, Shengping Li, Nan Liu, Congcong Chen, Qiaoyan Zhang, Shuai Wang, Haifeng Zhang, Xiaoliang Li, Ye Research Center for Biomedical Imaging Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen Guang Dong China Chongqing University of Technology Department of Biomedical Engineering Chongqing China Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States UCSF/UC Berkeley Joint Graduate Group in Bioengineering San FranciscoCA94158 United States

ISBN: (纸本)9781728137261

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 1H, 19F, and 31P, 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 (1H/19F/31P) 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, B1+ 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 1H/19F/31P at ultrahigh magnetic field were investigated. © 2019 IEEE.

关键词： Magnetic resonance

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Subcellular western blotting of single cells

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Microsystems & Nanoengineering 2017年第1期3卷 405-413页

作者： Kevin A.Yamauchi Amy E.Herr Department of Bioengineering University of CaliforniaBerkeleyCA 94720USA The UC Berkeley—UCSF Graduate Program in Bioengineering University of CaliforniaBerkeleyCA 94720USA

Although immunoassays are the de facto standard for determining subcellular protein localization in individual cells,antibody probe cross-reactivity and fixation artifacts remain confounding *** enhance selectivity while providing single-cell resolution,we introduce a subcellular western blotting technique capable of separately assaying proteins in the 14 pL cytoplasm and 2 pL nucleus of individual *** confer precision fluidic control,we describe a passive multilayer microdevice that leverages the rapid transport times afforded by *** isolating single cells in microwells,we apply single-cell differential detergent fractionation to lyse and western blot the cytoplasmic lysate,whereas the nucleus remains intact in the ***,we lyse the intact nucleus and western blot the nuclear *** index each protein analysis to the originating subcellular compartment,we utilize bi-directional electrophoresis,a multidimensional separation that assays the lysate from each compartment in a distinct region of the separation ***-cell bi-directional electrophoresis eliminates the need for semi-subjective image segmentation algorithms required in *** subcellular,single-cell western blot is demonstrated for six targets per cell,and successfully localizes spliceosome-associated proteins solubilized from large protein and RNA complexes,even for closely sized proteins(a 7 kDa difference).Measurement of NF-κB translocation dynamics in unfixed cells at 15-min intervals demonstrates reduced technical variance compared with *** chemical cytometry assay directly measures the nucleocytoplasmic protein distribution in individual unfixed cells,thus providing insight into protein signaling in heterogeneous cell populations.

关键词： cytometry microfluidic design proteomics single-cell analysis

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Glucocorticoids cause mandibular bone fragility and suppress osteocyte perilacunar-canalicular remodeling

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Bone Reports 2018年 9卷 145-153页

作者： Alemi, A. Sean Mazur, Courtney M. Fowler, Tristan W. Woo, Jonathon J. Knott, P. Daniel Alliston, Tamara Department of Otorhinolaryngology Head and Neck Surgery University of California San Francisco United States Department of Orthopaedic Surgery University of California San Francisco United States UC Berkeley-UCSF Graduate Program in Bioengineering United States

Osteocytes support dynamic, cell-intrinsic resorption and deposition of bone matrix through a process called perilacunar/canalicular remodeling (PLR). In long bones, PLR depends on MMP13 and is tightly regulated by PTH, sclerostin, TGFβ, and glucocorticoids. However, PLR is regulated differently in the cochlea, suggesting a mechanism that is anatomically distinct. Unlike long bones, the mandible derives from neural crest and exhibits unique susceptibility to medication and radiation induced osteonecrosis. Therefore, we sought to determine if PLR in the mandible is suppressed by glucocorticoids, as it is in long bone. Hemimandibles were collected from mice subcutaneously implanted with prednisolone or vehicle containing pellets for 7, 21, or 55 days (n = 8/group) for radiographic and histological analyses. Within 21 days, micro-computed tomography revealed a glucocorticoid-dependent reduction in bone volume/total volume and trabecular thickness and a significant decrease in bone mineral density after 55 days. Within 7 days, glucocorticoids strongly and persistently repressed osteocytic expression of the key PLR enzyme MMP13 in both trabecular and cortical bone of the mandible. Cathepsin K expression was significantly reduced only after 55 days of glucocorticoid treatment, at which point histological analysis revealed a glucocorticoid-dependent reduction in the lacunocanalicular surface area. In addition to reducing bone mass and suppressing PLR, glucocorticoids also reduced the stiffness of mandibular bone in flexural tests. Thus, osteocyte PLR in the neural crest-derived mandible is susceptible to glucocorticoids, just as it is in the mesodermally-derived femur, highlighting the need to further study PLR as a target of drugs, and radiation in mandibular osteonecrosis. © 2018

关键词： Glucocorticoids Mandible Osteocyte Perilacunar/canalicular remodeling

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QSMGAN: Improved quantitative susceptibility mapping using 3d generative adversarial networks with increased receptive field

arXiv

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arXiv 2019年

作者： Chen, Yicheng Jakary, Angela Hess, Christopher P. Lupo, Janine UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley University of California San Francisco California San FranciscoCA94158 Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States

Quantitative susceptibility mapping (QSM) is a powerful MRI technique that has shown great potential in quantifying tissue susceptibility in numerous neurological disorders. However, the intrinsic ill-posed dipole inversion problem greatly affects the accuracy of the susceptibility map. We proposed QSMGAN: A 3D deep convolutional neural network approach based on improved U-Net with increased phase receptive field and further refined the network using the WGAN-GP training strategy. Our method could generate accurate and realistic QSM from single orientation phase maps efficiently and performed significantly better than traditional non-learning-based dipole inversion algorithms. Copyright © 2019, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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