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Correction to: Toward Automatic Detection of Radiation-Induced Cerebral Microbleeds Using a 3D Deep Residual Network

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Journal of digital imaging 2019年第5期32卷 898页

作者： Yicheng Chen Javier E Villanueva-Meyer Melanie A Morrison Janine M Lupo UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Janine.Lupo@ucsf.edu. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. Janine.Lupo@ucsf.edu.

This paper was published inadvertently as open access. It has been corrected online.

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Iterative Motion Compensation reconstruction ultra-short TE(iMoCo UTE) for high resolution free breathing pulmonary MRI

arXiv

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arXiv 2020年

作者： Zhu, Xucheng Chan, Marilynn Lustig, Michael Johnson, Kevin Larson, Peder E.Z. UCSF/UC Berkeley Graduate Program in Bioengineering University of California San Francisco San FranciscoCA United States Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA United States Department of Pediatrics Division of Pediatric Pulmonology University of California San Francisco San FranciscoCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Department of Medical Physics University of Wisconsin Madison MadisonWI United States Department of Radiology University of Wisconsin Madison MadisonWI United States

Purpose: To develop a high scanning efficiency, motion corrected imaging strategy for free-breathing pulmonary MRI by combining a motion compensation reconstruction with a UTE acquisition, called iMoCo UTE. Methods: An optimized golden angle ordering radial UTE sequence was used to continuously acquire data for 5 minutes. All readouts were grouped to different respiratory motion states based on self-navigator signals, then motion resolved data was reconstructed by XD Golden-angle RAdial Sparse Parallel reconstruction (XD-GRASP). One state from the motion resolved images was selected as a reference, and motion fields from the other states to the reference were derived via non-rigid registration. Finally, all motion resolved data and motion fields were reconstructed by using an iterative motion compensation reconstruction with a total generalized variation sparse constraint. Results: The iMoCo UTE strategy was evaluated in volunteers and non-sedated pediatric patient(4-6 y/o) studies. Images reconstructed with iMoCo UTE provided sharper anatomical lung structures, and higher apparent SNR and CNR, compared to using other motion correction strategies, such as soft-gating, motion resolved reconstruction, and non-rigid motion compensation(MoCo). iMoCo UTE also showed promising results in an infant study. Conclusions: The proposed iMoCo UTE combines self-navigation, motion modeling, and a compressed sensing reconstruction to increase scan efficiency, SNR, and reduce respiratory motion in lung MRI. This proposed strategy shows improvements in free breathing lung MRI scans, especially in very challenging application situations, such as pediatric MRI studies. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Author Correction: Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

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Light, science & applications 2023年第1期12卷 93页

作者： Kyrollos Yanny Nick Antipa William Liberti Sam Dehaeck Kristina Monakhova Fanglin Linda Liu Konlin Shen Ren Ng Laura Waller UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA 94720 USA. kyrollosyanny@***. Department of Electrical Engineering & Computer Sciences University of California Berkeley CA 94720 USA. naantipa@***. Department of Electrical Engineering & Computer Sciences University of California Berkeley CA 94720 USA. TIPs Department Université libre de Bruxelles (ULB) 1050 Brussels Belgium. UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA 94720 USA.

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An agent-based model of epithelial cell cystogenesis implemented with a cellular Potts model

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Journal of Critical Care 2009年第3期24卷 e32-e33页

作者： Engelberg, Jesse A. Kim, Minji Mostov, Keith E. Hunt, C. Anthony UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California San Francisco CA 94143 USA Department of Anatomy University of California San Francisco CA 94143 USA Department of Bioengineering and Therapeutic Sciences University of California San Francisco CA 94143 USA

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A complete allosteric map of a GTPase switch in its native cellular network

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Cell Systems 2023年第3期14卷 237-246.e7页

作者： Mathy, Christopher J.P. Mishra, Parul Flynn, Julia M. Perica, Tina Mavor, David Bolon, Daniel N.A. Kortemme, Tanja Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco 94158 CA United States Quantitative Biosciences Institute University of California San Francisco San Francisco 94158 CA United States The UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco San Francisco 94158 CA United States Department of Biochemistry and Molecular Biotechnology University of Massachusetts Medical School Worcester 01605 MA United States Chan Zuckerberg Biohub San Francisco 94158 CA United States School of Life Sciences University of Hyderabad Telangana Hyderabad India

Allosteric regulation is central to protein function in cellular networks. A fundamental open question is whether cellular regulation of allosteric proteins occurs only at a few defined positions or at many sites distributed throughout the structure. Here, we probe the regulation of GTPases—protein switches that control signaling through regulated conformational cycling—at residue-level resolution by deep mutagenesis in the native biological network. For the GTPase Gsp1/Ran, we find that 28% of the 4,315 assayed mutations show pronounced gain-of-function responses. Twenty of the sixty positions enriched for gain-of-function mutations are outside the canonical GTPase active site switch regions. Kinetic analysis shows that these distal sites are allosterically coupled to the active site. We conclude that the GTPase switch mechanism is broadly sensitive to cellular allosteric regulation. Our systematic discovery of new regulatory sites provides a functional map to interrogate and target GTPases controlling many essential biological processes. © 2023 The Authors

关键词： allostery cellular regulation Gsp1 GTPases mutational scanning protein networks Ran

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Theoretical design and evaluation of endoluminal ultrasound applicators for thermal therapy of pancreatic cancer under image guidance

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AIP Conference Proceedings 2017年第1期1821卷

作者： Matthew Adams Serena Scott Vasant Salgaonkar Graham Sommer Chris Diederich 1Thermal Therapy Research Group University of California San Francisco 2340 Sutter Street S341 San Francisco CA 94109 USA 2Joint Graduate Program in Bioengineering UC Berkeley and UC San Francisco USA 3Stanford Medical Center 300 Pasteur Drive Stanford CA 94305 USA

An image-guided endoluminal ultrasound applicator has been proposed for palliative and potential curative thermal therapy of pancreatic tumors. By considering a directional transducer array of planar, tubular, or curvilinear transducers, this design offers the potential for fast volumetric therapy and 3D spatial control over the energy deposition profile. Treatment of pancreatic tumor tissue would be performed in a minimally invasive fashion with the applicator positioned in the gastrointestinal (GI) lumen, and sparing of the luminal wall would be achieved with a water-cooled balloon surrounding the transducers. A theoretical evaluation of this design was performed by developing a 3D acoustic and bioheat transfer model, with temperature and thermal dose solutions obtained using a FEM solver (COMSOL Multiphysics). Parametric studies were performed on a generalized anatomical model of the pancreas, tumor, and adjacent luminal wall to determine preferred transducer configurations and frequencies for maximizing lesion volume and penetration while sparing the luminal wall. Patient-specific models of pancreatic tumors were generated from CT studies and used to assess the feasibility of performing thermal ablation or hyperthermia on small (∼2 cm diameter) pancreatic head tumors with an endoluminal applicator positioned within the duodenum. Simulation results indicate lower transducer operating frequencies (1-3 MHz) are necessary to mitigate damage to the luminal wall, and a tradeoff between penetration depth and lesion volume emerges as the degree of focusing increases. For patient-specific ablation modeling of tumors within 30 mm of the luminal wall, approximately 95% of the volume could be ablated within 15 min using a planar or lightly focused transducer configuration without duodenal damage. Over 90% of the volume could be elevated above 40°C at steady state for hyperthermia applications (e.g., radiation sensitization, drug delivery) using a tubular transducer. For tum

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Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch

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Nature 2020年第7798期579卷 E8页

作者： Andrew H Ng Taylor H Nguyen Mariana Gómez-Schiavon Galen Dods Robert A Langan Scott E Boyken Jennifer A Samson Lucas M Waldburger John E Dueber David Baker Hana El-Samad Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA USA. Department of Bioengineering University of California Berkeley Berkeley CA USA. The UC Berkeley-UCSF Graduate Program in Bioengineering UC Berkeley Berkeley CA USA. Cell Design Initiative University of California San Francisco CA USA. Department of Biochemistry University of Washington Seattle WA USA. Institute for Protein Design University of Washington Seattle WA USA. Graduate Program in Biological Physics Structure and Design University of Washington Seattle WA USA. Howard Hughes Medical Institute University of Washington Seattle WA USA. Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA USA. hana.el-samad@ucsf.edu. Cell Design Initiative University of California San Francisco CA USA. hana.el-samad@ucsf.edu. Chan-Zuckerberg Biohub San Francisco CA USA. hana.el-samad@ucsf.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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

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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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Experimental investigations of an endoluminal ultrasound applicator for MR-guided thermal therapy of pancreatic cancer

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AIP Conference Proceedings 2017年第1期1821卷

作者： Matthew Adams Vasant Salgaonkar Peter Jones Juan Plata Henry Chen Kim Butts Pauly Graham Sommer Chris Diederich 1Thermal Therapy Research Group University of California San Francisco 2340 Sutter Street S341 San Francisco CA 94109 USA 2Joint Graduate Program in Bioengineering UC Berkeley and UC San Francisco USA 3Radiological Sciences Laboratory Stanford University 1201 Welch Road Palo Alto CA 94304 USA 4Stanford Medical Center 300 Pasteur Drive Stanford CA 94305 USA

An MR-guided endoluminal ultrasound applicator has been proposed for palliative and potential curative thermal therapy of pancreatic tumors. Minimally invasive ablation or hyperthermia treatment of pancreatic tumor tissue would be performed with the applicator positioned in the gastrointestinal (GI) lumen, and sparing of the luminal tissue would be achieved with a water-cooled balloon surrounding the ultrasound transducers. This approach offers the capability of conformal volumetric therapy for fast treatment times, with control over the 3D spatial deposition of energy. Prototype endoluminal ultrasound applicators have been fabricated using 3D printed fixtures that seat two 3.2 or 5.6 MHz planar or curvilinear transducers and contain channels for wiring and water flow. Spiral surface coils have been integrated onto the applicator body to allow for device localization and tracking for therapies performed under MR guidance. Heating experiments with a tissue-mimicking phantom in a 3T MR scanner were performed and demonstrated capability of the prototype to perform volumetric heating through duodenal luminal tissue under real-time PRF-based MR temperature imaging (MRTI). Additional experiments were performed in ex vivo pig carcasses with the applicator inserted into the esophagus and aimed towards liver or soft tissue surrounding the spine under MR guidance. These experiments verified the capacity of heating targets up to 20-25 mm from the GI tract. Active device tracking and automated prescription of imaging and temperature monitoring planes through the applicator were made possible by using Hadamard encoded tracking sequences to obtain the coordinates of the applicator tracking coils. The prototype applicators have been integrated with an MR software suite that performs real-time device tracking and temperature monitoring.

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Corrigendum: Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue

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Letters in applied microbiology 2017年第4期65卷 343页

作者： I Choopara N Arunrut W Kiatpathomchai D Dean N Somboonna Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok Thailand. Bioengineering and Sensing Technology Laboratory National Center for Genetic Engineering and Biotechnology Khlong Nueng Khlong Luang Pathum Thani Thailand. Center for Immunobiology and Vaccine Development UCSF Benioff Children's Hospital Oakland Research Institute Oakland CA USA. Department of Medicine University of California San Francisco CA USA. Joint Graduate Program in Bioengineering University of California Berkeley CA USA. Department of Microbiology Faculty of Science Chulalongkorn University Bangkok Thailand.

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