Article
Astronomy & Astrophysics
Sreemanti Chakraborti, Jonathan L. Feng, James K. Koga, Mauro Valli
Summary: The gamma factory proposal aims to produce high-energy photon beams at the LHC for discovering weakly-interacting particles. It has the potential to detect couplings lower than other terrestrial experiments and complements astrophysical observations.
Article
Engineering, Biomedical
Kevin Treb, York Haemisch, Christer Ullberg, Ran Zhang, Ke Li
Summary: This article presents a hybrid photon counting-energy integrating flat panel detector (FPD) design for upgrading interventional imaging. By replacing the central scintillator and thin-film transistor elements with a semiconductor photon counting detector (PCD) module, the imaging capabilities of the C-arm system can be improved while maintaining full field-of-view coverage. Experimental results show that this hybrid detector design can improve spatial resolution and contrast in vascular imaging, and provide seamless full field imaging. This design offers a cost-effective option for upgrading C-arm systems without compromising the clinical need for full field-of-view imaging.
PHYSICS IN MEDICINE AND BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ferdinand Otto, Xing Sun, Florian Schulz, Carlos Sanchez-Cano, Neus Feliu, Fabian Westermeier, Wolfgang J. Parak
Summary: X-ray photon correlation spectroscopy is used to determine the hydrodynamic diameters of gold nanoparticles in biological environments, providing an in situ method that overcomes the limitations of traditional visible light detection techniques.
Article
Nuclear Science & Technology
Bin Qin, Xu Liu, Qu-Shan Chen, Dong Li, Wen-Jie Han, Ping Tan, Zhong-Qi Zhang, Chong Zhou, Ao-Te Chen, Yi-Cheng Liao, Wei Wang
Summary: The paper discusses the design considerations and implementation of a proton therapy facility at Huazhong University of Science and Technology, including beam optics, high-order aberrations, energy/intensity modulation, and orbit correction. It also introduces the technical implementation of main beamline components and subsystems.
NUCLEAR SCIENCE AND TECHNIQUES
(2021)
Article
Engineering, Biomedical
Kevin Treb, Jeff Radtke, Wesley S. Culberson, Ke Li
Summary: In photon counting detectors, the accumulation of electric pulses induced by multiple x-ray photons can lead to count losses. This study introduces an inexpensive readout circuit element to collect time-integrated charge to correct for pile-up-induced count losses. Experimental results demonstrate that this correction method can restore the count accuracy of paralyzable photon counting detectors, without impacting the spatial resolution of the images.
PHYSICS IN MEDICINE AND BIOLOGY
(2023)
Article
Materials Science, Coatings & Films
Nils Martensson, Alexander Foehlisch, Svante Svensson
Summary: This article reviews the importance of the development of modern photoelectron spectroscopy, with a special focus on the research at Uppsala University and at Berkeley. The influence of two pioneers, Kai Siegbahn and Dave Shirley, is highlighted. The early interaction between the two centers helped to kick-start the field, and both laboratories continue to play a crucial role in creating new experimental capabilities and developing the theoretical understanding of spectroscopic processes.
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A
(2022)
Article
Computer Science, Interdisciplinary Applications
Xu Ji, Mang Feng, Kevin Treb, Ran Zhang, Sebastian Schafer, Ke Li
Summary: Modern interventional x-ray systems are often equipped with flat-panel detector-based cone-beam CT (FPD-CBCT) for high spatial resolution imaging. This study introduced a photon-counting detector (PCD) to C-arm systems as a supplementary option, providing high quality, spectral imaging capabilities. Experimental results showed that PCD-CT images had improved image quality and quantitative imaging capabilities compared to FPD-CBCT images at the same dose level.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Physics, Multidisciplinary
Johannes Moeller, Mario Reiser, Joerg Hallmann, Ulrike Boesenberg, Alexey Zozulya, Hendrik Rahmann, Anna-Lena Becker, Fabian Westermeier, Thomas Zinn, Michael Sprung, Theyencheri Narayanan, Christian Gutt, Anders Madsen
Summary: The X-ray speckle visibility spectroscopy (XSVS) technique has been successfully applied to study the dynamics of radiation sensitive biological samples at low doses, allowing for the observation of static, frozen speckle patterns. This technique, when combined with new generation X-ray sources, shows great potential for further investigations of protein dynamics.
NEW JOURNAL OF PHYSICS
(2021)
Article
Instruments & Instrumentation
Kotaro Ishiji, Kazuya Kobayashi, Masanori Hidaka, Hidenobu Taguchi, Kenichiro Sakamoto, Kumiko Konishi, Akio Shima, Toshihiro Okajima
Summary: In this study, the authors used a synchrotron beam at the SAGA Light Source facility to expand the beam width for high-efficiency experiments of deep X-ray lithography, radiation mutation breeding, and X-ray topography. The reconstructed experimental setup demonstrated improved experimental efficiency and the advantages of using expanded beams.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT
(2022)
Article
Physics, Multidisciplinary
Yunzhu Wang, Xiaohao Dong, Jun Hu
Summary: This paper investigates the feasibility of using sapphire crystal to make CRL and compares it with other common materials. The calculation and simulation results show that sapphire lenses have better performance, achieving smaller spot sizes with higher intensity and minimal thermal effects.
FRONTIERS IN PHYSICS
(2022)
Article
Physics, Condensed Matter
Eliot Gann, Thomas Crofts, Glenn Holland, Peter Beaucage, Terry McAfee, R. Joseph Kline, Brian A. Collins, Christopher R. McNeill, Daniel A. Fischer, Dean M. DeLongchamp
Summary: This article introduces a polarized resonant soft x-ray scattering (RSoXS) station designed and built by the National Institute of Standards and Technology, located at the National Synchrotron Light Source-II (NSLS-II) in Brookhaven National Laboratory, New York. The station is optimized for measurements on soft matter systems, with a focus on minimizing beam damage and maximizing collection efficiency of polarized x-rays, utilizing novel optical design, sample manipulator and sample environments, and detector setups.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Instruments & Instrumentation
Josef Hormes, Wantana Klysubun, Jost Goettert, Henning Lichtenberg, Alexey Maximenko, Kevin Morris, Pawel Nita, Alexander Prange, Jacek Szade, Lasse Wagner, Marcin Zajac
Summary: The new X-ray absorption spectroscopy beamline at the National Synchrotron Radiation Centre SOLARIS has a fixed exit beam Lemmonier type monochromator, allowing the coverage of the desired energy range with different crystal sets. It is a high vacuum system, enabling quick crystal changes and minimizing photon absorption.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS
(2021)
Article
Nuclear Science & Technology
Jian-Feng Ji, Han Guo, Yan-Ling Xue, Rong-Chang Chen, Ya-Nan Fu, Guo-Hao Du, Biao Deng, Hong-Lan Xie, Ti-Qiao Xiao
Summary: A new X-ray imaging and biomedical application beamline (BL13HB) has been implemented at the Shanghai Radiation Synchrotron Facility (SSRF) to facilitate 2D and 3D static and dynamic X-ray imaging. BL13HB utilizes a super-bending magnet as the X-ray source and is equipped with new equipment to accommodate various experimental methods. The experimental station of the beamline is specifically designed for in situ dynamic experiments and has been open to users since June 2021.
NUCLEAR SCIENCE AND TECHNIQUES
(2023)
Article
Instruments & Instrumentation
Kenichi Ozawa, Yoshihiro Aiura, Daisuke Wakabayashi, Hirokazu Tanaka, Takashi Kikuchi, Akio Toyoshima, Kazuhiko Mase
Summary: Beamline 13 of the Photon Factory, which has been operating since 2010, is used for vacuum ultraviolet and soft X-ray experiments. The recent upgrades allow for microscopic measurements, with improved beam performance and focusing. The use of an advanced planar polarized light emitter II undulator and a renewed toroidal post-mirror enhance the capabilities of the beamline.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Instruments & Instrumentation
G. S. Peters, Yu A. Gaponov, P. Konarev, M. A. Marchenkova, K. B. Ilina, V. V. Volkov, Yu Pisarevsky, M. Kovalchuk
Summary: Technical and methodological work was conducted to improve the quality of experiments at the BioMUR small-angle X-ray scattering (SAXS) beamline at the Kurchatov synchrotron radiation source. The installation and testing of scatterless slits, as well as the replacement of outdated windows, resulted in a significant improvement in the signal-to-noise ratio of the SAXS experiments.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT
(2022)
Article
Biochemical Research Methods
Ryuichi Kato, Masahiko Hiraki, Yusuke Yamada, Mikio Tanabe, Toshiy Senda
Summary: The PXS system is a fully automated protein crystallization and monitoring system that can automatically set up crystallization plates, transfer, observe, and monitor crystallization drops. As time has passed, user demands have changed, requiring screening with smaller amounts of proteins, and membrane proteins have become a primary target for X-ray crystallography.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Takahiro Doi, Hideaki Takagi, Nobutaka Shimizu, Noriyuki Igarashi, Shinichi Sakurai
Summary: This study investigated the relationship between the mechanical properties and structure of block copolymers mixed with tackifiers of different solubilities. The results showed that the type of tackifier used had a significant impact on the nanostructure and mechanical properties, with stress-relaxation behavior being explained through fitting with three-component exponent functions. The study also clarified the hierarchy of structures contributing to stress-relaxation behavior.
Article
Multidisciplinary Sciences
Ebru Destan, Busra Yuksel, Bradley B. Tolar, Esra Ayan, Sam Deutsch, Yasuo Yoshikuni, Soichi Wakatsuki, Christopher A. Francis, Hasan DeMirci
Summary: The protein encoded by Nmar_1308 plays a crucial role in the ammonia-oxidizing thaumarchaeal 3HP/4HB cycle by acting as both CCAH and 3HPD, thereby reducing the number of enzymes required for CO2 fixation and lowering the overall cost of biosynthesis. The high-resolution crystal structure of this bifunctional enzyme provides insights into key catalytic residues in the thaumarchaeal 3HP/4HB pathway.
SCIENTIFIC REPORTS
(2021)
Article
Instruments & Instrumentation
Kentaro Harada, Nobumasa Funamori, Naoto Yamamoto, Yoshito Shimosaki, Miho Shimada, Tsukasa Miyajima, Kensei Umemori, Hiroshi Sakai, Norio Nakamura, Shogo Sakanaka, Yukinori Kobayashi, Tohru Honda, Shunsuke Nozawa, Hironori Nakao, Yasuhiro Niwa, Daisuke Wakabayashi, Kenta Amemiya, Noriyuki Igarashi
Summary: A hybrid ring with a superconducting-linac injector is proposed as a highly flexible synchrotron radiation source. It allows simultaneous use of storage (SR) and single-pass (SP) beams, enabling unique experiments and research in various fields. The extendability of the Hybrid Ring suggests its potential development into a synchrotron radiation complex.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Chemistry, Multidisciplinary
Kaiming Zhang, Naoki Horikoshi, Shanshan Li, Alexander S. Powers, Mikhail A. Hameedi, Grigore D. Pintilie, Hee-Don Chae, Yousuf A. Khan, Carl-Mikael Suomivuori, Ron O. Dror, Kathleen M. Sakamoto, Wah Chiu, Soichi Wakatsuki
Summary: In this study, a protein double shell was engineered to overcome the size limitation of determining structures of flexible proteins smaller than 30 kDa. This approach successfully determined the structure of the 11 kDa KIX domain of CBP, and molecular dynamics simulations were used to design peptides that block protein-protein interactions. The findings provide insights for the development of next-generation inhibitors.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Irimpan I. Mathews, Naoki Horikoshi, Tsutomu Matsui, Manat Kaur, Soichi Wakatsuki, Daria Mochly-Rosen, Adriana Ann Garcia
Summary: This study identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP(+) and dimer complex, suggesting potential therapeutic strategies for G6PD deficiency. The connection between allosteric NADP+ binding, oligomerization, and pathogenicity was elucidated, and stabilizing the dimer and tetramer was found to improve protein stability and activity. These findings provide a foundation for future drug discovery efforts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Instruments & Instrumentation
Daisuke Wakabayashi, Yoshio Suzuki, Yuki Shibazaki, Hiroshi Sugiyama, Keiichi Hirano, Ryutaro Nishimura, Kazuyuki Hyodo, Noriyuki Igarashi, Nobumasa Funamori
Summary: In this paper, a variable-magnification full-field x-ray microscope using two Fresnel zone plates (FZPs) is proposed. The positions of the two FZPs can be adjusted to continuously change the magnification, even if the sample and camera positions are fixed. Experimental results demonstrate that the magnification can be changed in the range of 25-150x using a hard x-ray beam, and high magnification can be achieved at a short camera length.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Instruments & Instrumentation
Keiichi Hirano, Hiroshi Sugiyama, Ryutaro Nishimura, Daisuke Wakabayashi, Yoshio Suzuki, Noriyuki Igarashi, Nobumasa Funamori
Summary: A zoom function is proposed for an X-ray analyzer-based optics that allows observation of samples with different types of contrast. Asymmetrically cut crystals were used to implement the zoom function, and proof-of-principle experiments showed that the image quality at higher magnification was superior. This achievement has the potential to advance research in various fields such as materials science and biomedical science.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Chemistry, Multidisciplinary
Hasan DeMirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vogeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmueller, Tobias J. Erb, Esteban Vohringer-Martinez, Soichi Wakatsuki
Summary: This study used various experimental methods to investigate the structural organization of ECR in Kitasatospora setae, and found that its catalytic activity is carried out by a pair of dimers. The results reveal the dynamic organization and synchronized inter- and intrasubunit communications of this enzyme during catalysis.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemical Research Methods
Alexei S. Soares, Yusuke Yamada, Jean Jakoncic, Sean McSweeney, Robert M. Sweet, John Skinner, James Foadi, Martin R. Fuchs, Dieter K. Schneider, Wuxian Shi, Babak Andi, Lawrence C. Andrews, Herbert J. Bernstein
Summary: KAMO and BLEND are effective tools for managing the merging of large numbers of data sets in serial crystallography. By extending BLEND to support additional clustering options and using more accurate distance metrics, it is possible to reduce the need for manual intervention in the process. This increases sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets based on intensity or amplitude differences.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mikhail Ali Hameedi, Erica T. Prates, Michael R. Garvin, Irimpan Mathews, B. Kirtley Amos, Omar Demerdash, Mark Bechthold, Mamta Iyer, Simin Rahighi, Daniel W. Kneller, Andrey Kovalevsky, Stephan Irle, Van-Quan Vuong, Julie C. Mitchell, Audrey Labbe, Stephanie Galanie, Soichi Wakatsuki, Daniel Jacobson
Summary: The authors report on the crystallographic and computational studies that explain how SARS-CoV-2 3CLpro cleaves NF-kappa B Essential Modulator, a host protein, in addition to its viral substrates. They discuss the association between this cleavage and the high adaptability of SARS-CoV-2 in humans. The study provides insights into the binding mechanism between 3CLpro and NEMO, as well as the role of key binding residues in the fitness of SARS-CoV-2.
NATURE COMMUNICATIONS
(2022)
Meeting Abstract
Hematology
John Dalloul, Minyoung Youn, Kailen Mark, Alexander Powers, Ron Dror, Soichi Wakatsuki, Kathleen M. Sakamoto
Article
Multidisciplinary Sciences
Nai-Chi Chen, Chun-Hsiung Wang, Masato Yoshimura, Yi-Qi Yeh, Hong-Hsiang Guan, Phimonphan Chuankhayan, Chien-Chih Lin, Pei-Ju Lin, Yen-Chieh Huang, Soichi Wakatsuki, Meng-Chiao Ho, Chun-Jung Chen
Summary: Understanding the structural diversity of honeybee-infecting viruses is crucial for protecting pollinator health and managing disease spread in ecology and agriculture. This study used cryo-EM to determine the structures of T=4 and T=3 capsids of Lake Sinai virus (LSV) 2 and delta-N48 LSV1. The analysis revealed unique structural features and interactions of the capsid proteins, as well as the impact of pH on capsid conformations and particle sizes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Brian C. Sanders, Suman Pokhrel, Audrey D. Labbe, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson, Gwyndalyn Phillips, Kevin L. Weiss, Qiu Zhang, Hugh O'Neill, Manat Kaur, Jurgen G. Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E. Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W. Moriarty, Paul D. Adams, Andrzej Joachimiak, Brett L. Hurst, Suresh Kumar, Tauseef R. Butt, Colleen B. Jonsson, Lori Ferrins, Soichi Wakatsuki, Stephanie Galanie, Martha S. Head, Jerry M. Parks
Summary: Designed a series of protease inhibitors targeting SARS-CoV-2, with the most effective inhibitor capable of blocking viral replication in mammalian cells and showing no significant inhibition of human proteases. These findings present an opportunity for the development of protease inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
James S. Davies, Michael J. Currie, Rachel A. North, Mariafrancesca Scalise, Joshua D. Wright, Jack M. Copping, Daniela M. Remus, Ashutosh Gulati, Dustin R. Morado, Sam A. Jamieson, Michael C. Newton-Vesty, Gayan S. Abeysekera, Subramanian Ramaswamy, Rosmarie Friemann, Soichi Wakatsuki, Jane R. Allison, Cesare Indiveri, David Drew, Peter D. Mace, Renwick C. J. Dobson
Summary: The researchers report the structure of the TRAP transporter and propose a model for substrate transport using an 'elevator-with-an-operator' mechanism.
NATURE COMMUNICATIONS
(2023)
