Article
Multidisciplinary Sciences
Shiro Ihara, Hikaru Saito, Mizumo Yoshinaga, Lavakumar Avala, Mitsuhiro Murayama
Summary: This study presents an image correction framework based on deep learning for addressing distortion and noise issues in STEM image acquisition. Experimental results demonstrate that DL enables rapid and high-quality STEM image acquisition with high spatio-temporal resolution.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Chen Huang, Judy S. Kim, Angus I. Kirkland
Summary: There is a need for characterisation techniques that provide detailed information about structure-function relationships in biology. In this review, the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions is explored, discussing its progress, limitations, and potential areas for future development in both single particle analysis and applications to heterogeneous large objects.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ulf Nyman, Peter Leander, Per Liss, Gunnar Sterner, Torkel Brismar
Summary: Glomerular filtration rate (GFR) is the best index to evaluate kidney function and its use is recommended to assess the risk of iodine contrast medium-induced acute kidney injury (CI-AKI). GFR can be expressed in absolute terms (mL/min) or adjusted to body surface area (mL/min/1.73 m(2)). Absolute GFR represents the excretion capacity, while relative GFR is used to assess the degree of kidney damage and sensitivity for CI-AKI.
EUROPEAN RADIOLOGY
(2023)
Article
Multidisciplinary Sciences
Domenica Farci, Patrycja Haniewicz, Dario Piano
Summary: The study found that the S-layer in Deinococcus radiodurans has crystalline regularity in all layers of the cell envelope, indicating its importance as a structural and functional scaffold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
John Sedat, Angus McDonald, Hu Cang, Joseph Lucas, Muthuvel Arigovindan, Zvi Kam, Cornelis Murre, Michael Elbaum
Summary: Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has revealed a large-scale chromosome structure. This study further investigates and analyzes these structures, proposing a unified architecture for interphase chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Minh Pham, Yakun Yuan, Arjun Rana, Stanley Osher, Jianwei Miao
Summary: Tomography has revolutionized the fields of physical, biological, and medical sciences. The mathematical foundation of tomography involves reconstructing a 3D object from a set of 2D projections. The main challenge in tomography is achieving accurate 3D reconstructions from a limited number of noisy projections. The RESIRE algorithm has been developed as a real-space iterative reconstruction method that outperforms other existing algorithms in terms of accuracy and can be widely applied in various tomography applications.
SCIENTIFIC REPORTS
(2023)
Article
Biology
Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen
Summary: The study reveals the structure of Photosystem II in solution at 1.95 angstrom resolution using single-particle cryo-electron microscopy, with a visible PsbY subunit and reduced electron beam damage by lowering the dosage, providing valuable insights for determining damage-free cryo-EM structures.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kapil Gupta, Christine Toelzer, Maia Kavanagh Williamson, Deborah K. Shoemark, A. Sofia F. Oliveira, David A. Matthews, Abdulaziz Almuqrin, Oskar Staufer, Sathish K. N. Yadav, Ufuk Borucu, Frederic Garzoni, Daniel Fitzgerald, Joachim Spatz, Adrian J. Mulholland, Andrew D. Davidson, Christiane Schaffitzel, Imre Berger
Summary: The BriS Delta variant of SARS-CoV-2, with a deletion in a spike cleavage site, shows altered infectivity and cell tropism due to the deletion in the spike structure. This study provides insights into how this deletion affects viral characteristics and interactions with host cells, indicating potential evolutionary trajectories within the same infected host.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Pei Tong, Avneesh Gautam, Ian W. Windsor, Meghan Travers, Yuezhou Chen, Nicholas Garcia, Noah B. Whiteman, Lindsay G. A. McKay, Nadia Storm, Lauren E. Malsick, Anna N. Honko, Felipe J. N. Lelis, Shaghayegh Habibi, Simon Jenni, Yongfei Cai, Linda J. Rennick, W. Paul Duprex, Kevin R. McCarthy, Christy L. Lavine, Teng Zuo, Junrui Lin, Adam Zuiani, Jared Feldman, Elizabeth A. MacDonald, Blake M. Hauser, Anthony Griffths, Michael S. Seaman, Aaron G. Schmidt, Bing Chen, Donna Neuberg, Goran Bajic, Stephen C. Harrison, Duane R. Wesemann
Summary: Memory B cell reserves can produce protective antibodies against SARS-CoV-2, but the impact on variants is unclear. Studying antibodies from convalescent individuals revealed seven major antibody competition groups, important for neutralizing the virus.
Article
Biochemistry & Molecular Biology
Linhua Tai, Guoliang Yin, Fei Sun, Yun Zhu
Summary: The nuclear pore complex (NPC) is a large protein assembly that penetrates the nuclear membrane. Recent breakthroughs in cryo-EM and artificial intelligence-based modeling have allowed for improved understanding of the complex structure of the NPC. This review article summarizes the history and latest advancements in studying the architecture of the NPC, as well as future directions for research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Engineering, Multidisciplinary
Changsheng Zhang, Guogang Zhu, Jian Fu, Gang Zhao
Summary: Phase contrast computed tomography (PCCT) provides excellent imaging contrast on soft tissue by generating absorption, phase and dark-field contrast tomographic images, showing great potential in clinical diagnosis. However, existing PCCT methods require high radiation doses. This paper proposes a deep learning (DL) framework for low dose PCCT based on inter-contrast enhancement, utilizing the multi-contrast feature of PCCT and the varying effects of noise on each contrast. Experimental validation on grating-based PCCT demonstrates a significant quality improvement of multi-contrast tomographic images, indicating the potential of DL techniques in low dose PCCT.
Article
Chemistry, Multidisciplinary
Eunju Cha, Hyungjin Chung, Jaeduck Jang, Junho Lee, Eunha Lee, Jong Chul Ye
Summary: This article presents an unsupervised deep learning method for high-angle annular dark-field scanning transmission electron microscopy-energy dispersive X-ray tomography. The proposed method provides high-quality reconstruction results even under low-dose and sparse-view conditions.
Article
Radiology, Nuclear Medicine & Medical Imaging
Thomas P. W. van den Boogert, Ricardo R. Lopes, Nick H. J. Lobe, Tim A. Verwest, Jaap Stoker, Jose P. Henriques, Henk A. Marquering, R. Nils Planken
Summary: The study aimed to evaluate a patient-tailored contrast delivery protocol for CTCA and found that adjusting the IDR can improve luminal attenuation and significantly reduce the total iodine load. Additionally, the peak height of the test-bolus scan was associated with luminal attenuation in certain cases.
JOURNAL OF THORACIC IMAGING
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Cathrine Helgestad Kristiansen, Owen Thomas, Thien Trung Tran, Sumit Roy, Dan Levi Hykkerud, Audun Sanderud, Jonn Terje Geitung, Peter M. Lauritzen
Summary: The study compared the vascular attenuation of an experimental half iodine-load dual-layer spectral detector CT (SDCT) lower limb CTA with a control group of standard iodine-load conventional 120-kVp CTA. The results showed that the experimental group had higher vascular attenuation at 40 keV and lower vascular attenuation at 50 keV compared to the control group. Additionally, the experimental group had better image noise, contrast-to-noise ratio, signal-to-noise ratio, and subjective examination quality at both 40 keV and 50 keV.
EUROPEAN RADIOLOGY
(2023)
Article
Biochemical Research Methods
Pawel Ossowski, Arkadiusz Kus, Wojciech Krauze, Szymon Tamborski, Michal Ziemczonok, Lukasz Kuzbicki, Maciej Szkulmowski, Malgorzata Kujawinska
Summary: This paper presents a holographic tomography technique that uses wavelength and illumination scanning in the near-infrared region to acquire projections. The study shows that the multi-wavelength protocol has advantages in terms of signal-to-noise ratio and contrast-to-noise ratio over single-wavelength protocols, even with the same number of projections used for reconstruction. Furthermore, the approach is suitable for providing high-quality refractive index distributions of relatively thick colon cancer samples.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Multidisciplinary Sciences
Nobuhiro Iwakura, Takeshi Yokoyama, Fabio Quaglia, Kaoru Mitsuoka, Kazuhiro Mio, Hideki Shigematsu, Mikako Shirouzu, Akira Kaji, Hideko Kaji
Article
Microscopy
Kazuhiro Aoyama, Kotaro Nagano, Kaoru Mitsuoka
Article
Multidisciplinary Sciences
Kotaro Tanaka, Shuichi Takeda, Kaoru Mitsuoka, Toshiro Oda, Chieko Kimura-Sakiyama, Yuichiro Maeda, Akihiro Narita
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Atsuko Nakanishi, Jun-ichi Kishikawa, Masatada Tamakoshi, Kaoru Mitsuoka, Ken Yokoyama
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Ayumi Koike-Takeshita, Kaoru Mitsuoka, Hideki Taguchi
JOURNAL OF BIOLOGICAL CHEMISTRY
(2014)
Article
Microscopy
Kazutoshi Tani, Christopher P. Arthur, Masatada Tamakoshi, Ken Yokoyama, Kaoru Mitsuoka, Yoshinori Fujiyoshi, Christoph Gerle
Article
Biochemistry & Molecular Biology
Goki Tanaka, Tomoyuki Yamanaka, Yoshiaki Furukawa, Naoko Kajimura, Kaoru Mitsuoka, Nobuyuki Nukina
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Goki Tanaka, Tomoyuki Yamanaka, Yoshiaki Furukaw, Naoko Kajimura, Kaoru Mitsuoka, Nobuyuki Nukina
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2019)
Article
Biochemistry & Molecular Biology
Tomohito Yamada, Toru Yoshida, Akihiro Kawamoto, Kaoru Mitsuoka, Kenji Iwasaki, Hideaki Tsuge
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Multidisciplinary Sciences
J. Kishikawa, A. Nakanishi, A. Nakano, S. Saeki, A. Furuta, T. Kato, K. Mistuoka, K. Yokoyama
Summary: The authors report the atomic models of 18 catalytic intermediates of the V-1 domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not immediately rotate after the binding of ATP, but undergoes multiple events including ATP hydrolysis and release of ADP and Pi during the rotation process.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Atsuko Nakanishi, Jun-ichi Kishikawa, Kaoru Mitsuoka, Ken Yokoyama
Summary: This study used cryo-electron microscopy to reveal the intermediate structures of V/A-ATPase during the transition from the ground state to the steady state, providing insights into the sequential binding of ATP to its catalytic sites. These findings enhance our understanding of the initial activation processes of enzymes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Review
Biophysics
Atsuko Nakanishi, Jun-ichi Kishikawa, Kaoru Mitsuoka, Ken Yokoyama
BIOPHYSICS AND PHYSICOBIOLOGY
(2019)
