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Machine learning for improved current-density reconstruction from two-dimensional vector magnetic images

Physical Review Applied 2025年第3期23卷 034035-034035页

作者： Niko R. Reed Danyal Bhutto Matthew J. Turner Declan M. Daly Sean M. Oliver Jiashen Tang Kevin S. Olsson Nicholas Langellier Mark J.H. Ku Department of Physics University of Maryland College Park Maryland USA Quantum Technology Center University of Maryland College Park Maryland USA Joint Quantum Institute University of Maryland College Park Maryland USA Department of Biomedical Engineering Boston University Boston Massachusetts USA A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Massachusetts USA Department of Electrical and Computer Engineering University of Maryland College Park Maryland USA The MITRE Corporation McLean Virginia 22102 USA Intelligence Community Postdoctoral Research Fellowship Program University of Maryland College Park Maryland 20742 USA Department of Physics Harvard University Cambridge Massachusetts USA Present address: VideaHealth Inc. Boston MA. Department of Materials Science and Engineering University of Delaware Newark Delaware 19716 USA Department of Physics and Astronomy University of Delaware Newark Delaware 19716 USA Present address: Northrop Grumman Mission Systems Linthicum Maryland 21090 USA.

The reconstruction of electrical current densities from magnetic field measurements is an important technique with applications in materials science, circuit design, quality control, plasma physics, and biology. Analytic reconstruction methods exist for planar currents, but break down in the presence of high-spatial-frequency noise or large standoff distance, restricting the types of systems that can be studied. Here, we demonstrate the use of a deep convolutional neural network for current density reconstruction from two-dimensional images of vector magnetic fields acquired by a quantum diamond microscope . Trained network performance significantly exceeds analytic reconstruction for data with high noise or large standoff distances. This machine learning technique can perform quality inversions on lower-signal-to-noise-ratio data, significantly reducing the data collection time and permitting reconstructions of weaker and three-dimensional current sources.

关键词： Signal to noise ratio

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Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors

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Biophysical Reviews 2020年第2期12卷 323-332页

作者： Murata, Takeshi Yasuda, Satoshi Hayashi, Tomohiko Kinoshita, Masahiro Graduate School of Science Chiba University 1-33 Yayoi-cho Inage Chiba 263-8522 Japan Molecular Chirality Research Center Chiba University 1-33 Yayoi-cho Inage Chiba 263-8522 Japan Institute of Advanced Energy Kyoto University Uji Kyoto 611-0011 Japan Present address: Interdisciplinary Program of Biomedical Engineering Assistive Technology and Art and Sports Sciences Faculty of Engineering Niigata University 8050 Ikarashi 2-no-cho Nishi-ku Niigata 950-2181 Japan

Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor;a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen;and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of N_BW = 3.39 (N_BW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT_2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed. © 2020, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： G-protein-coupled receptor Integral equation theory Lipid bilayer Membrane protein Morphometric approach Protein folding Solvation thermodynamics Thermostabilizing mutation

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GCN2 inhibition reduces mutant SOD1 clustering and toxicity and delays disease progression in an amyotrophic lateral sclerosis mouse model

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Translational Neurodegeneration 2024年第1期13卷 351-355页

作者： Didio Alberto Ortiz Nuria Peregrín Miguel Valencia Rodrigo Vinueza-Gavilanes Elisa Marín-Ordovas Roberto Ferrero María Jesús Nicolás Gloria González-Aseguinolaza Montserrat Arrasate Tomás Aragón DNA and RNA Medicine Program Center for Applied Medical Research(CIMA)University of NavarraPamplonaSpain Biomedical Engineering Program Center for Applied Medical Research(CIMA)University of NavarraPamplonaSpain Institute of Data Science and Artificial Intelligence(DATAI) University of NavarraPamplonaSpain Navarra Institute for Health Research(IdiSNA) PamplonaSpain Neuroimmunology Department Multiple Sclerosis Center of Catalonia(Cemcat)Vall d’Hebron Research Institute(VHIR)BarcelonaSpain School of Medicine University of NavarraPamplonaSpain Brain Lab Biobizkaia Health Research InstituteBarakaldoSpain Present Address:Ikerbasque Basque Foundation for ScienceBilbaoSpain

Main text The disruption of protein folding homeostasis in motoneurons(MNs)and the accumulation of protein aggregates are some of the main molecular hallmarks of amyotrophic lateral sclerosis(ALS).Evidence from sporadic and familial ALS(fALS)patients and from ALS models suggests that protein aggregation directly participates in *** turn,the loss of MN homeostasis triggers a coping mechanism,the integrated stress response(ISR)[1].The ISR is initiated by four independent stress-sensing kinases,each of them activated by distinct stresses:protein kinase R(PKR)by double-strand RNA,protein kinase RNA-like endoplasmic reticulum kinase(PERK)by protein misfolding at the endoplasmic reticulum(ER),general control nonderepressible 2(GCN2)by nutrient starvation,and heme-regulated inhibitor(HRI)by heme deprivation.

关键词： homeostasis amyotrophic sclerosis

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Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates

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Cell 2025年

作者： Xiao Yan David Kuster Priyesh Mohanty Jik Nijssen Karina Pombo-García Jorge Garcia Morato Azamat Rizuan Titus M Franzmann Aleksandra Sergeeva Anh M Ly Feilin Liu Patricia M Passos Leah George Szu-Huan Wang Jayakrishna Shenoy Helen L Danielson Busra Ozguney Alf Honigmann Yuna M Ayala Nicolas L Fawzi Dennis W Dickson Wilfried Rossoll Jeetain Mittal Simon Alberti Anthony A Hyman Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Dresden 01307 Saxony Germany. Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX 77843 USA. Department of Neuroscience Mayo Clinic Jacksonville FL 32224 USA. Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering Technische Universität Dresden Dresden 01307 Saxony Germany. Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Dresden 01307 Saxony Germany Edward Doisy Department of Biochemistry and Molecular Biology Saint Louis University St. Louis MO 63104 USA. Department of Molecular Biology Cell Biology & Biochemistry Brown University Providence RI 02912 USA. Center for Biomedical Engineering Brown University Providence RI 02912 USA. Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX 77843 USA Department of Chemistry Texas A&M University College Station TX 77843 USA Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station TX 77843 USA. Electronic address: jeetain@tamu.edu. Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering Technische Universität Dresden Dresden 01307 Saxony Germany. Electronic address: simon.alberti@tu-dresden.de. Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Dresden 01307 Saxony Germany. Electronic address: hyman@mpi-cbg.de.

Cytosolic aggregation of the nuclear protein TAR DNA-binding protein 43 (TDP-43) is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43-enriched phase within stress granules, which subsequently transition into pathological aggregates. Intra-condensate demixing of TDP-43 is observed in iPS-motor neurons, a disease mouse model, and patient samples. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We suggest that up-concentration inside condensates followed by intra-condensate demixing could be a general pathway for protein aggregation.

关键词： ALS FTD TDP-43 biomolecular condensate intra-condensate demixing neurodegenerative diseases oxidative stress phase separation protein aggregation stress granules

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Neural Electrodes: Interfacing Conducting Polymer Nanotubes with the Central Nervous System: Chronic Neural Recording using Poly(3,4‐ethylenedioxythiophene) Nanotubes (Adv. Mater. 37/2009)

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Advanced Materials 2009年第37期21卷

作者： Mohammad Reza Abidian Kip A. Ludwig Timothy C. Marzullo David C. Martin Daryl R. Kipke Department of Biomedical Engineering The University of Michigan 1101 Beal Ave. Ann Arbor MI 48109 (USA) Department of Biomedical Engineering The University of Michigan Ann Arbor MI 48109 (USA) Neuroscience Program The University of Michigan Ann Arbor MI 48109 (USA) Department of Materials Science and Engineering Macromolecular Science and Engineering and Biomedical Engineering Ann Arbor MI 48109 (USA) Present Address: Karl W. Böer Professor and Chair Materials Science and Engineering The University of Delaware 201C DuPont Hall Newark DE 19716 (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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Corrigendum to "Metal-organic frameworks, NH2-MIL-88(Fe), as carriers for ophthalmic delivery of brimonidine" [Acta Biomater. 79 (2018) 344-353]

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Acta biomaterialia 2019年 85卷 321页

作者： Se-Na Kim Chun Gwon Park Beom Kang Huh Seung Ho Lee Chang Hee Min Yun Young Lee Young Kook Kim Ki Ho Park Young Bin Choy Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul 08826 Republic of Korea. Department of Biomedical Engineering SKKU Institute for Convergence Sungkyunkwan University (SKKU) Suwon 16419 Republic of Korea. Institute of Medical & Biological Engineering Medical Research Center Seoul National University Seoul 03080 Republic of Korea. Department of Biomedical Engineering Seoul National University College of Medicine Seoul 03080 Republic of Korea. Department of Ophthalmology Seoul National University Hospital Seoul 03080 Republic of Korea Department of Ophthalmology Seoul National University College of Medicine Seoul 03080 Republic of Korea. Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul 08826 Republic of Korea Institute of Medical & Biological Engineering Medical Research Center Seoul National University Seoul 03080 Republic of Korea Department of Biomedical Engineering Seoul National University College of Medicine Seoul 03080 Republic of Korea. Electronic address: ybchoy@snu.ac.kr.

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Frontispiz: Visualizing Microglia with a Fluorescence Turn‐On Ugt1a7c Substrate

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Angewandte Chemie 2019年第24期131卷

作者： Beomsue Kim Masahiro Fukuda Jung‐Yeol Lee Dongdong Su Srikanta Sanu Aymeric Silvin Audrey T. T. Khoo Taejoon Kwon Xiao Liu Weijie Chi Xiaogang Liu Sejong Choi Diana S. Y. Wan Sung‐Jin Park Jin‐Soo Kim Florent Ginhoux H. Shawn Je Young‐Tae Chang Singapore Bioimaging Consortium Agency for Science Technology and Research (A*STAR) Singapore 138667 Singapore Program in Neuroscience and Behavioral Disorders Duke-NUS Medical School Singapore 169857 Singapore Department of Chemistry Pohang University of Science and Technology Pohang 37673 Korea Present address: New drug discovery center DGMIF Daegu 41061 Korea Singapore Immunology Network A*STAR Singapore 138648 Singapore Department of Biomedical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Korea Center for Self-assembly and Complexity Institute for Basic Science (IBS) Pohang 37673 Korea Singapore University of Technology and Design Singapore 487372 Singapore Department of Chemistry Seoul National University Seoul 08826 Korea Center for Genome Engineering IBS Daejeon 34047 Korea

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Visualizing Microglia with a Fluorescence Turn‐On Ugt1a7c Substrate

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Angewandte Chemie 2019年第24期131卷

Microglia, the brain‐resident macrophage, are involved in brain development and contribute to the progression of neural disorders. Despite the importance of microglia, imaging of live microglia at a cellular resolution has been limited to transgenic mice. Efforts have therefore been dedicated to developing new methods for microglia detection and imaging. Using a thorough structure–activity relationships study, we developed CDr20, a high‐performance fluorogenic chemical probe that enables the visualization of microglia both in vitro and in vivo. Using a genome‐scale CRISPR‐Cas9 knockout screen, the UDP‐glucuronosyltransferase Ugt1a7c was identified as the target of CDr20. The glucuronidation of CDr20 by Ugt1a7c in microglia produces fluorescence.

关键词： Biologische Aktivität Fluoreszsonden Kontrastmittel Mikroglia Struktur-Aktivitäts-Bezieung

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Frontispiece: Visualizing Microglia with a Fluorescence Turn-On Ugt1a7c Substrate

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Angewandte Chemie International Edition 2019年第24期58卷

作者： Dr. Beomsue Kim Dr. Masahiro Fukuda Dr. Jung-Yeol Lee Dr. Dongdong Su Dr. Srikanta Sanu Dr. Aymeric Silvin Audrey T. T. Khoo Prof. Taejoon Kwon Xiao Liu Dr. Weijie Chi Prof. Xiaogang Liu Sejong Choi Diana S. Y. Wan Dr. Sung-Jin Park Prof. Jin-Soo Kim Prof. Florent Ginhoux Prof. H. Shawn Je Prof. Young-Tae Chang Singapore Bioimaging Consortium Agency for Science Technology and Research (A*STAR) Singapore 138667 Singapore Program in Neuroscience and Behavioral Disorders Duke-NUS Medical School Singapore 169857 Singapore Department of Chemistry Pohang University of Science and Technology Pohang 37673 Korea Present address: New drug discovery center DGMIF Daegu 41061 Korea Singapore Immunology Network A*STAR Singapore 138648 Singapore Department of Biomedical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Korea Center for Self-assembly and Complexity Institute for Basic Science (IBS) Pohang 37673 Korea Singapore University of Technology and Design Singapore 487372 Singapore Department of Chemistry Seoul National University Seoul 08826 Korea Center for Genome Engineering IBS Daejeon 34047 Korea

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