68 results on '"Yonekura K"'
Search Results
2. Complementary use of electron and X-ray microcrystallography to reveal quantum structural information of organic molecules
- Author
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Takaba, K., primary, Maki-Yonekura, S., additional, Inoue, I., additional, Tono, K., additional, Yabashi, M., additional, and Yonekura, K., additional
- Published
- 2023
- Full Text
- View/download PDF
3. High-throughput and high-resolution 3D-ED structure analysis through AI-based data collection and hybrid approach
- Author
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Maki-Yonekura, S., primary, Takaba, K., additional, Kawakami, K., additional, and Yonekura, K., additional
- Published
- 2023
- Full Text
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4. Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
- Author
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Kawakami, K., primary, Maki-Yonekura, S., additional, Hamaguchi, T., additional, Takaba, K., additional, and Yonekura, K., additional
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- 2023
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5. Structure of the Anabaena PSI-monomer-IsiA supercomplex
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Nagao, R., primary, Kato, K., additional, Hamaguchi, T., additional, Kawakami, K., additional, Yonekura, K., additional, and Shen, J.R., additional
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- 2023
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6. Electron crystallographic structure of TIA-1 prion-like domain, wild type sequence
- Author
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Takaba, K., primary, Maki-Yonekura, S., additional, Sekiyama, N., additional, Imamura, K., additional, Kodama, T., additional, Tochio, H., additional, and Yonekura, K., additional
- Published
- 2022
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- View/download PDF
7. Electron crystallographic structure of TIA-1 prion-like domain, A381T mutant
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Takaba, K., primary, Maki-Yonekura, S., additional, Sekiyama, N., additional, Imamura, K., additional, Kodama, T., additional, Tochio, H., additional, and Yonekura, K., additional
- Published
- 2022
- Full Text
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8. Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus
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Kawakami, K., primary, Hamaguchi, T., additional, Hirose, Y., additional, Kosumi, D., additional, Miyata, M., additional, Kamiya, N., additional, and Yonekura, K., additional
- Published
- 2022
- Full Text
- View/download PDF
9. Phycocyanin rod structure of cyanobacterial phycobilisome
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Kawakami, K., primary, Hamaguchi, T., additional, Hirose, Y., additional, Kosumi, D., additional, Miyata, M., additional, Kamiya, N., additional, and Yonekura, K., additional
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- 2022
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10. Cryo-EM structure of a primordial cyanobacterial photosystem I
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Kato, K., primary, Hamaguchi, T., additional, Nagao, R., additional, Kawakami, K., additional, Yonekura, K., additional, and Shen, J.R., additional
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- 2022
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11. A new method for producing superior set yogurt, focusing on heat treatment and homogenization
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Ichimura, T., primary, Osada, T., additional, Yonekura, K., additional, and Horiuchi, H., additional
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- 2022
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12. Structure of endothelin ET B receptor-G i complex in a conformation stabilized by unique NPxxL motif.
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Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, and Doi T
- Subjects
- Humans, Amino Acid Motifs, Cryoelectron Microscopy, GTP-Binding Protein alpha Subunits, Gi-Go chemistry, GTP-Binding Protein alpha Subunits, Gi-Go metabolism, GTP-Binding Protein alpha Subunits, Gi-Go ultrastructure, GTP-Binding Protein alpha Subunits, Gi-Go genetics, HEK293 Cells, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Receptor, Endothelin B metabolism, Receptor, Endothelin B chemistry
- Abstract
Endothelin type B receptor (ET
B R) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ETB R activation by the endogenous peptide hormones endothelin (ET)-1-3 stimulates several signaling pathways, including Gs , Gi/o , Gq/11 , G12/13 , and β-arrestin. Although the conserved NPxxY motif in transmembrane helix 7 (TM7) is important during GPCR activation, ETB R possesses the lesser known NPxxL motif. In this study, we present the cryo-EM structure of the ETB R-Gi complex, complemented by MD simulations and functional studies. These investigations reveal an unusual movement of TM7 to the intracellular side during ETB R activation and the essential roles of the diverse NPxxL motif in stabilizing the active conformation of ETB R and organizing the assembly of the binding pocket for the α5 helix of Gi protein. These findings enhance our understanding of the interactions between GPCRs and G proteins, thereby advancing the development of therapeutic strategies., (© 2024. The Author(s).)- Published
- 2024
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13. Bexarotene-induced hypothyroidism and dyslipidemia; a nation-wide study.
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Manaka K, Sato J, Hikima Y, Horikoshi H, Taguchi M, Morita A, Suga H, Boki H, Fujimura T, Hirai Y, Shimauchi T, Tateishi C, Kiyohara E, Muto I, Nakajima H, Abe R, Fujii K, Nishigori C, Nakano E, Yonekura K, Funakoshi T, Amano M, Miyagaki T, Yamashita R, Sugaya M, Hamada T, Nangaku M, Iiri T, and Makita N
- Subjects
- Humans, Male, Female, Middle Aged, Retrospective Studies, Aged, Japan epidemiology, Thyroxine blood, Triglycerides blood, Adult, Tetrahydronaphthalenes adverse effects, Tetrahydronaphthalenes therapeutic use, Aged, 80 and over, Anticarcinogenic Agents therapeutic use, Anticarcinogenic Agents adverse effects, Hypertriglyceridemia chemically induced, Bexarotene adverse effects, Hypothyroidism chemically induced, Hypothyroidism epidemiology, Dyslipidemias chemically induced
- Abstract
Central hypothyroidism and dyslipidemia are well-known adverse events (AEs) of bexarotene therapy. Although hypothyroidism is known to cause dyslipidemia, no study has examined the association between hypothyroidism and dyslipidemia in patients undergoing bexarotene therapy. The aim of this study is to examine this association. A retrospective observational study was performed among 294 patients who initiated bexarotene therapy in Japan (nation-wide postmarketing complete surveillance). Jonckheere-Terpstra (one sided) test was performed to evaluate the effect of the bexarotene dose on lipid metabolisms, and regression analyses were performed to evaluate associations of bexarotene dose, free thyroxine (FT4), body mass index (BMI), and lipid metabolisms. Most patients developed hypothyroidism. Two-third of patients showed FT4 values below the lower limit at 1 week. Triglycerides (TG) increased in a bexarotene dose-dependent manner, and grade ≥3 AEs on hypertriglyceridemia was observed in 39% of the patients. Additionally, one-third of grade ≥3 AEs on hypertriglyceridemia occurred within 1 week. The delta_FT4 (difference in FT4 from baseline) negatively correlated with TG increase at 1 week (p = 0.012) but not with low density lipoprotein cholesterol (LDL-C) increase at any week. Bexarotene-induced hypothyroidism is almost inevitable and occurred quickly. Bexarotene-induced hypertriglyceridemia showed positive bexarotene dose dependency and negative delta_FT4 dependency. Prophylactic and appropriate thyroid hormone compensation therapy and starting bexarotene at low doses with subsequent titration while managing dyslipidemia may have a beneficial effect for the successful continuation of bexarotene therapy without severe endocrine and metabolic AEs.
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- 2024
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14. Real-world safety and efficacy of biologics in elderly patients with psoriasis: A multicenter observational study.
- Author
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Ohata C, Anezaki H, Yanase T, Katayama E, Kaneko S, Saito K, Yamane M, Nakamaru S, Tsuruta N, Okazaki F, Ito K, Kikuchi S, Koike Y, Miyagi T, Sugita K, Nakahara T, Takezaki D, Saruwatari H, Yoshida Y, Yonekura K, Higashi Y, Sawada Y, Chinuki Y, Yamaguchi K, and Imafuku S
- Abstract
Clinical trials of biologics have frequently excluded elderly patients, resulting in inadequate data on their safety and efficacy. Additionally, evidence of their safety and efficacy remains limited, despite some real-world studies. To assess the safety and efficacy of biologics in elderly patients with psoriasis, we compared these outcomes in younger patients using data from the West Japan Psoriasis Registry (WJPR). The WJPR consists of approximately 30 facilities in Western Japan, including various healthcare settings. This study enrolled 1395 patients who participated in the 2022 follow-up survey of the WJPR and were either using or had used biologics during the survey. These included 456 patients in the elderly group (≥65 years) and 939 patients in the younger group (<65 years). Treatment-ending adverse events (TEAEs) occurred in 15.8% and 11.3% of elderly and younger patients, respectively. The incidence rate per 1000 patient-years (PY) for TEAEs was significantly higher in elderly patients than in younger patients (32.9 vs 23.2, p = 0.0234). Infectious diseases were more prevalent in the elderly group than the younger group; however, no significant difference in the frequency of infectious diseases was found between the two groups (p = 0.0807). Malignant neoplasms occurred significantly more frequently in the elderly group than in the younger group (p = 0.0169). Our results indicate a few concerns about infection when prescribing biologics to elderly patients. Biologics were effective for both elderly and younger patients. We found no significant differences in the proportion of patients with a body surface area score ≤3%, Physician's Global Assessment score 0/1, or Patient's Global Assessment score 0/1, as well as in the mean Dermatology Life Quality Index and the Itch Numerical Rating Scale between the younger and the elderly groups. Overall, our results confirm the appropriateness of using biologics in elderly patients with regard to safety and efficacy., (© 2024 Japanese Dermatological Association.)
- Published
- 2024
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15. Total Synthesis of the Sesquiterpene (-)-Merrillianin.
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Shiina I, Iizumi T, Taniguchi S, Sugimoto M, Shimazaki T, Yamai YS, Ogawa G, Yamada T, Shinohara S, Kageyama Y, Kuboki T, Suwa Y, Yonekura K, Ito K, Toyoyama K, Tateyama S, Mori T, and Murata T
- Abstract
The first total synthesis of (-)-merrillianin ( 1 ), which is a natural sesquiterpene with a tricyclic structure having a cyclopentane ring and five- and seven-membered lactone parts, is demonstrated. This asymmetric total synthesis enabled the absolute stereostructure determination of naturally occurring (-)- 1 .
- Published
- 2024
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16. Meroterpenes and prenylated benzoylphloroglucinol from the flowers of Hypericum formosanum.
- Author
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Tanaka N, Takizawa R, Shimomoto Y, Tsuji D, Yonekura K, Itoh K, Akagi R, and Kashiwada Y
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- Mice, Animals, Flowers, Microglia, Prenylation, Molecular Structure, Phloroglucinol pharmacology, Phloroglucinol chemistry, Hypericum chemistry
- Abstract
Formohyperins A-F, previously undescribed meroterpenes, and grandone, a prenylated benzoylphloroglucinol being considered to be one of their biogenetic precursors, were isolated from the flowers of a Hypericaceous plant, Hypericum formosanum Maxim. Detailed spectroscopic analyses showed that formohyperins A-D were meroterpenes with an enolized 3-phenylpropane-1,3-dione moiety. Formohyperins E and F were elucidated as meroterpenes having a 4-benzoyl-5-hydroxycyclopent-4-ene-1,3-dione moiety. Formohyperins A-C and E were optically active, and their absolute configurations were deduced by comparison of the experimental and TDDFT calculated ECD spectra. In contrast, formohyperin D was concluded to be a racemate. Formohyperins A-F and grandone were found to show inhibitory activities against LPS-stimulated IL-1β production from murine microglial cells with EC
50 values of 13.2, 6.6, 8.5, 24.3, 4.1, 10.9, and 3.0 μM, respectively., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)- Published
- 2024
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17. [A Long-Surviving Case of Locally Advanced Breast Cancer with Multiple Lung Metastasis].
- Author
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Satoh E, Innami Y, Uehira D, Yonekura K, Murakata A, Ohinata R, Toyofuku Y, Tanami H, Osanai T, Sugano N, and Sakoma T
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- Humans, Female, Aged, Time Factors, Carcinoma, Ductal, Breast secondary, Carcinoma, Ductal, Breast therapy, Carcinoma, Ductal, Breast drug therapy, Mastectomy, Breast Neoplasms pathology, Breast Neoplasms drug therapy, Lung Neoplasms secondary, Lung Neoplasms drug therapy, Antineoplastic Combined Chemotherapy Protocols therapeutic use
- Abstract
We report a case of right advanced breast cancer with multiple lung metastases in a 66-year-old woman. Her breast cancer( invasive ductal carcinoma, cT4bN1M1, Stage Ⅳ)was resected in October 2007(mastectomy plus axillary lymph node dissection)after local arterial infusion therapy(total dose 5-FU 4,735 mg plus adriamycin 180 mg), which caused bilateral lung arterial embolism due to deep vein thrombosis in right her leg. She had to be treated by anticoagulant therapy, mechanical ventilation and placement of IVC filter before her operation. Subsequent chemo-endocrine therapy(docetaxel 6 courses plus anastrozole)was continued. In October 2008, a CT scan showed disappearance of multiple lung metastases (complete response). In November 2015 (8 years after her operation), a CT scan showed recurrence of multiple lung metastases and endocrine therapy was changed to tamoxifen. A year later, a CT scan showed disappearance of multiple lung metastases(complete response)again and keep a condition of complete response in her breast cancer until May 2023 (15 years after her operation).
- Published
- 2024
18. Comparative bonding performance of coronal dentin disks and CAD/CAM resin composite disks for biological restoration: The impact of resin-coating technique.
- Author
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Ishihara H, Yonekura K, Ikeda M, Inoue G, Nakajima M, Shimada Y, and Hosaka K
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- Dental Cements, Tensile Strength, Materials Testing, Composite Resins chemistry, Dentin-Bonding Agents chemistry, Glass Ionomer Cements, Dentin, Resin Cements chemistry, Dental Bonding methods
- Abstract
This study evaluated the bonding performance of coronal dentin disks, designed for biological restoration, and CAD/CAM resin composite disks when bonded to flat dentin surfaces using dual-cure resin cements, with and without a resin-coating (RC) technique. Three distinct groups were established within the non-RC group, each using one of the two types of resin cements in a self-adhesive mode: one-step self-etch adhesive (1-SEA) without light-cure, 1-SEA with light-cure, and a separate group using an alternate cement. Within the RC group, a subgroup was established for each cement. The microtensile bond strength (μTBS) of the disk-dentin beam was tested after 0 and 10,000 thermocycles in a 5°C/55°C. No significant μTBS difference was observed among the non-RC groups. However, when using RC, the μTBSs of coronal dentin disks significantly exceeded those of CAD/CAM resin composite disks. Thermocycle aging did not affect μTBS in any of the bonding methods, except in self-adhesive mode.
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- 2024
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19. The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.
- Author
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Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, and Nagao R
- Subjects
- Phylogeny, Biological Evolution, Cryoelectron Microscopy, Photosystem I Protein Complex genetics, Rhodophyta genetics
- Abstract
Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae , whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI., Competing Interests: Competing interests statement:The authors declare no competing interest.
- Published
- 2024
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20. Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds.
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Takaba K, Maki-Yonekura S, Inoue I, Tono K, Fukuda Y, Shiratori Y, Peng Y, Morimoto J, Inoue S, Higashino T, Sando S, Hasegawa T, Yabashi M, and Yonekura K
- Abstract
There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.
- Published
- 2024
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21. Impaired humoral immunity following COVID-19 vaccination in HTLV-1 carriers.
- Author
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Kameda T, Utsunomiya A, Otsuka N, Kubuki Y, Uchida T, Shide K, Kamiunten A, Nakano N, Tokunaga M, Miyazono T, Ito Y, Yonekura K, Kawakita T, Akizuki K, Tahira Y, Karasawa M, Hidaka T, Konagata A, Taniguchi N, Nagatomo Y, Kogo F, Shimizu K, Ueno H, Ishizaki J, Takahashi N, Ikei Y, Hidaka M, Yamaguchi H, and Shimoda K
- Subjects
- Humans, Aged, COVID-19 Vaccines, Immunity, Humoral, Prospective Studies, Vaccination, Immunoglobulin G, Antibodies, Viral, Human T-lymphotropic virus 1, COVID-19 prevention & control, HTLV-I Infections, Hypertension, Diabetes Mellitus, Dyslipidemias
- Abstract
Background: Whether human T-lymphotropic virus type 1 (HTLV-1) carriers can develop sufficient humoral immunity after coronavirus disease 2019 (COVID-19) vaccination is unknown., Methods: To investigate humoral immunity after COVID-19 vaccination in HTLV-1 carriers, a multicenter, prospective observational cohort study was conducted at five institutions in southwestern Japan, an endemic area for HTLV-1. HTLV-1 carriers and HTLV-1-negative controls were enrolled for this study from January to December 2022. During this period, the third dose of the COVID-19 vaccine was actively administered. HTLV-1 carriers were enrolled during outpatient visits, while HTLV-1-negative controls included health care workers and patients treated by participating institutions for diabetes, hypertension, or dyslipidemia. The main outcome was the effect of HTLV-1 infection on the plasma anti-COVID-19 spike IgG (IgG-S) titers after the third dose, assessed by multivariate linear regression with other clinical factors., Results: We analyzed 181 cases (90 HTLV-1 carriers, 91 HTLV-1-negative controls) after receiving the third dose. HTLV-1 carriers were older (median age 67.0 vs. 45.0 years, p < 0.001) and more frequently had diabetes, hypertension, or dyslipidemia than did HTLV-1-negative controls (60.0% vs. 27.5%, p < 0.001). After the third dose, the IgG-S titers decreased over time in both carriers and controls. Multivariate linear regression in the entire cohort showed that time since the third dose, age, and HTLV-1 infection negatively influenced IgG-S titers. After adjusting for confounders such as age, or presence of diabetes, hypertension, or dyslipidemia between carriers and controls using the overlap weighting propensity score method, and performing weighted regression analysis in the entire cohort, both time since the third dose and HTLV-1 infection negatively influenced IgG-S titers., Conclusions: The humoral immunity after the third vaccination dose is impaired in HTLV-1 carriers; thus, customized vaccination schedules may be necessary for them., (© 2024. The Author(s).)
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- 2024
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22. Reinvestigation on primary processes of PSII-dimer from Thermosynechococcus vulcanus by femtosecond pump-probe spectroscopy.
- Author
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Kosumi D, Bandou-Uotani M, Kato S, Kawakami K, Yonekura K, and Kamiya N
- Subjects
- Chlorophyll A, Spectrum Analysis, Electron Transport, Carotenoids metabolism, Photosystem II Protein Complex metabolism, Chlorophyll metabolism, Thermosynechococcus, beta Carotene metabolism, Cyanobacteria metabolism
- Abstract
Cyanobacterial photosynthetic apparatus efficiently capture sunlight, and the energy is subsequently transferred to photosystem I (PSI) and II (PSII), to produce electrochemical potentials. PSII is a unique membrane protein complex that photo-catalyzes oxidation of water and majorly contains photosynthetic pigments of chlorophyll a and carotenoids. In the present study, the ultrafast energy transfer and charge separation dynamics of PSII from a thermophilic cyanobacterium Thermosynechococcus vulcanus were reinvestigated by femtosecond pump-probe spectroscopic measurements under low temperature and weak intensity excitation condition. The results imply the two possible models of the energy transfers and subsequent charge separation in PSII. One is the previously suggested "transfer-to-trapped limit" model. Another model suggests that the energy transfers from core CP43 and CP47 antennas to the primary electron donor Chl
D1 with time-constants of 0.71 ps and 3.28 ps at 140 K (0.17 and 1.33 ps at 296 K), respectively and that the pheophytin anion (PheoD1 ) is generated with the time-constant of 43.0 ps at 140 K (14.8 ps at 296 K) upon excitation into the Q- ) is generated with the time-constant of 43.0 ps at 140 K (14.8 ps at 296 K) upon excitation into the Qy band of chlorophyll a at 670 nm. The secondary electron transfer to quinone QA : PheoD1 - QA is observed with the time-constant of 650 ps only at 296 K. On the other hand, an inefficient β-carotene → chlorophyll a energy transfer (33%) occurred after excitation to the SD1 QA - is observed with the time-constant of 650 ps only at 296 K. On the other hand, an inefficient β-carotene → chlorophyll a energy transfer (33%) occurred after excitation to the S2 state of β-carotene at 500 nm. Instead, the carotenoid triplet state appeared in an ultrafast timescale after excitation at 500 nm., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)- Published
- 2024
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23. Author Correction: Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography.
- Author
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Takaba K, Maki-Yonekura S, Inoue I, Tono K, Hamaguchi T, Kawakami K, Naitow H, Ishikawa T, Yabashi M, and Yonekura K
- Published
- 2023
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24. Photoinduced α-Aminoalkylation of Sulfonylarenes with Alkylamines.
- Author
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Yonekura K, Aoki K, Nishida T, Ikeda Y, Oyama R, Hatano S, Abe M, and Shirakawa E
- Abstract
α-Aminoalkylation of sulfonylarenes with alkylamines was found to be induced by photoirradiation. Here various types of alkylamines, such as trialkylamines, dialkylamines, N,N-dialkylanilines and N-alkylanilines as well as sulfonylarenes containing an azole, azine, heterole or benzene ring are available. The reaction proceeds through a homolytic aromatic substitution (HAS) process consisting of addition of an α-aminoalkyl radical to a sulfonylarene and elimination of the sulfonyl radical to give the α-arylalkylamine, where photoirradiation is considered to induce homolysis of sulfonylarenes leading to the generation of α-aminoalkyl radicals that make a radical chain operative., (© 2023 Wiley-VCH GmbH.)
- Published
- 2023
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25. Applications and limitations of electron 3D crystallography.
- Author
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Yonekura K, Maki-Yonekura S, and Takaba K
- Subjects
- Crystallography methods, Crystallography, X-Ray, Microscopy, Electron, Transmission, Peptides, Electrons, Proteins chemistry
- Abstract
Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
- Published
- 2023
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26. Prognostic factors for primary cutaneous anaplastic large-cell lymphoma: a multicentre retrospective study from Japan.
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Miyagaki T, Inoue N, Kamijo H, Boki H, Takahashi-Shishido N, Suga H, Shimauchi T, Kiyohara E, Hirai Y, Yonekura K, Takeuchi K, and Sugaya M
- Subjects
- Humans, Retrospective Studies, Ki-1 Antigen, Prognosis, In Situ Hybridization, Fluorescence, Japan epidemiology, Lymphoma, Large-Cell, Anaplastic diagnosis, Lymphoma, Large-Cell, Anaplastic genetics, Lymphoma, Large-Cell, Anaplastic pathology, Skin Neoplasms pathology, Mycosis Fungoides pathology, Lymphomatoid Papulosis
- Abstract
Background: The clinical implications of DUSP22 rearrangement and the association between DUSP22 rearrangement and lymphoid enhancer-binding factor 1 (LEF1) expression pattern in CD30+ cutaneous T-cell lymphomas (CTCLs) are unknown., Objectives: This study assessed the incidence of DUSP22 rearrangement and its clinical and immunohistochemical implications in primary cutaneous anaplastic large-cell lymphoma (pcALCL), lymphomatoid papulosis (LyP) and CD30+ mycosis fungoides with large-cell transformation (MF-LCT), focusing especially on the association with the prognosis and LEF1 expression pattern. Prognostic factors of pcALCL were also examined., Methods: We conducted a multicentre retrospective study including patients with pcALCL, LyP and MF-LCT diagnosed between 1 January 2000 and 31 December 2018 in Japan. Baseline data at diagnosis, treatment course, overall survival (OS) and disease-specific survival (DSS) were collected. Immunohistochemical analysis and fluorescence in situ hybridization to detect DUSP22 and TP63 rearrangement were performed using skin samples at diagnosis. We investigated the association between staining pattern and these gene rearrangements. We also assessed the prognostic implications of clinical status, immunohistochemical results and the presence of gene rearrangements., Results: DUSP22 rearrangement was detected in 50% (11 of 22) of cases of pcALCL, but not in any cases with LyP (0 of 14) or MF-LCT (0 of 11). TP63 rearrangement was not detected in any case. Clinically, patients with pcALCL with DUSP22 rearrangement did not tend to develop ulcers (P = 0.081). There was no significant association between DUSP22 rearrangement status and immunohistochemical results, including LEF1 expression pattern. T3 stage and the presence of lower limb lesions were significantly associated with shorter OS (P = 0.012 and 0.021, respectively, by log-rank test). Similarly, they were significantly correlated with shorter DSS (P = 0.016 and 0.0001, respectively)., Conclusions: DUSP22 rearrangement is relatively specific to pcALCL among CD30+ CTCLs in Japan. Although the LEF1 expression pattern was not related to DUSP22 rearrangement in pcALCL, there was no rearrangement if LEF1 was not expressed. We confirmed that T3 stage and the lower limb involvement were significantly associated with decreased OS and DSS. The presence or absence of lower limb lesions should be included in T-stage subcategorization in the future., Competing Interests: Conflicts of interest: The authors have no conflicts of interest to declare., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Association of Dermatologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2023
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27. Digitally Guided Direct Composite Injection Technique with a Bi-layer Clear Mini-Index for the Management of Extensive Occlusal Caries in a Pediatric Patient: A Case Report.
- Author
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Hosaka K, Tichy A, Yamauti M, Watanabe K, Kamoi K, Yonekura K, Foxton R, and Nakajima M
- Subjects
- Humans, Child, Adolescent, Composite Resins chemistry, Resin Cements chemistry, Antioxidants, Dental Restoration, Permanent, Dentin-Bonding Agents chemistry, Dental Cements chemistry, Dental Caries Susceptibility
- Abstract
Purpose: This case report presents a direct composite inverse injection technique using a bi-layer clear mini-index fabricated with a digital workflow to restore extensive posterior occlusal cavities in a 13-year-old patient., Materials and Methods: After a root canal treatment in the right mandibular first molar and step-wise excavation of deep caries in the left mandibular first molar, the extensive occlusal restorations were digitally designed using CAD software, upon which digital wax-ups were 3D-printed. Bi-layer clear mini-indices consisting of a hard outer plastic layer and an elastic inner silicone layer were prepared from the 3D-printed cast. The bonding surfaces were deproteinized using a 6% sodium hypochlorite solution, and an antioxidant (Clearfil DC Activator; Kuraray Noritake) was utilized to improve the dentin bonding durability of a 2-step self-etch adhesive (Clearfil SE Bond 2; Kuraray Noritake). Subsequently, a highly filled universal-shade flowable resin composite (RC) was incrementally placed into the cavities. To create the final occlusal morphology, the same RC was inversely injected through the opening of the bi-layer indices., Results: The workflow was feasible, and the occlusal cavities were efficiently restored using the injection technique. Occlusal carving and adjustments of the morphology were not necessary, leading to less chair time. At the 1-year follow-up, the clinical outcome was excellent., Conclusion: The injection technique with a bi-layer clear mini-index accurately translated the digital wax-ups into large, final restorations. Precise morphology and shortened chair time enhanced patient satisfaction, but at the expense of multiple visits.
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- 2023
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28. Nonsupersymmetric Heterotic Branes.
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Kaidi J, Ohmori K, Tachikawa Y, and Yonekura K
- Abstract
The common statement that any consistent quantum gravity theory contains dynamical objects with all possible charges suggests that there are still a number of hitherto-unidentified branes in string theory. Here we give the exact worldsheet description of near-horizon limits of nonsupersymmetric p-branes in ten-dimensional Spin(32)/Z_{2} or (E_{8}×E_{8})⋊Z_{2} heterotic superstring theories for p=7, 6, 4, 0.
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- 2023
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29. Electrochemical Direct α-Arylation of Alkylamines with Sulfonylarenes.
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Yonekura K, Murooka M, Aoki K, and Shirakawa E
- Abstract
The electrochemical α-arylation of alkylamines with sulfonylarenes has been developed. Here, diverse trialkylamines and aryl(dimethyl)amines are applicable to the α-arylation with sulfonylarenes having an azole, azine, and benzene nucleus. The α-arylation was scaled up using an electrolysis flow cell. Mechanistic studies show that anodic oxidation of an alkylamine with a sulfinate as a mediator followed by deprotonation gives an α-aminoalkyl radical, which undergoes homolytic aromatic substitution (HAS) on a sulfonylarene to give the corresponding α-arylalkylamine.
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- 2023
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30. Restoration of a Microdont Using the Resin Composite Injection Technique With a Fully Digital Workflow: A Flexible 3D-printed Index With a Stabilization Holder.
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Watanabe K, Tichy A, Kamoi K, Hiasa M, Yonekura K, Tanaka E, Nakajima M, and Hosaka K
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- Humans, Workflow, Silicones, Printing, Three-Dimensional, Esthetics, Dental, Composite Resins therapeutic use
- Abstract
Direct composite restorations are accepted as a treatment option for microdontia, which is a relatively prevalent condition that poses esthetic concerns. While free-hand composite placement is technique-sensitive and time-consuming, the resin composite injection technique is more straightforward and predictable. A fully digital workflow has been recently introduced, but the 3D-printed resin index is rigid and challenged by undercuts, as opposed to the silicone index. This case report presents a flexible 3D-printed resin index, which can accurately transfer the digitally simulated functional and esthetic form to the final restoration. In addition, a rigid stabilization holder was designed to stabilize the flexible index., (©Operative Dentistry, 2023.)
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- 2023
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31. Correction to "First Total Synthesis of Tanzawaic Acid B".
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Murata T, Tsutsui H, Yoshida T, Kubota H, Hiraishi S, Natsukawa H, Suzuki Y, Hiraga D, Mori T, Maekawa Y, Tateyama S, Toyoyama K, Ito K, Suzuki K, Yonekura K, Shibata N, Sato T, Tasaki Y, Inohana T, Takano A, Egashira N, Honda M, Umezaki Y, and Shiina I
- Abstract
[This corrects the article DOI: 10.1021/acsomega.3c03634.]., (© 2023 The Authors. Published by American Chemical Society.)
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- 2023
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32. Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect.
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Aizawa H, Sato T, Maki-Yonekura S, Yonekura K, Takaba K, Hamaguchi T, Minato T, and Yamamoto HM
- Abstract
Enantioselectivity of helical aggregation is conventionally directed either by its homochiral ingredients or by introduction of chiral catalysis. The fundamental question, then, is whether helical aggregation that consists only of achiral components can obtain enantioselectivity in the absence of chiral catalysis. Here, by exploiting enantiospecific interaction due to chiral-induced spin selectivity (CISS) that has been known to work to enantio-separate a racemic mixture of chiral molecules, we demonstrate the enantioselectivity in the assembly of mesoscale helical supramolecules consisting of achiral cobalt phthalocyanines. The helical nature in our supramolecules is revealed to be mesoscopically incorporated by dislocation-induced discretized twists, unlike the case of chiral molecules whose chirality are determined microscopically by chemical bond. The relevance of CISS effect in the discretized helical supramolecules is further confirmed by the appearance of spin-polarized current through the system. These observations mean that the application of CISS-based enantioselectivity is no longer limited to systems with microscopic chirality but is expanded to the one with mesoscopic chirality., (© 2023. The Author(s).)
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- 2023
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33. First Total Synthesis of Tanzawaic Acid B.
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Murata T, Tsutsui H, Yoshida T, Kubota H, Hiraishi S, Natsukawa H, Suzuki Y, Hiraga D, Mori T, Maekawa Y, Tateyama S, Toyoyama K, Ito K, Suzuki K, Yonekura K, Shibata N, Sato T, Tasaki Y, Inohana T, Takano A, Egashira N, Honda M, Umezaki Y, and Shiina I
- Abstract
The first total synthesis of (+)-tanzawaic acid B, a natural polyketide bearing a pentadienoic ester and octalin moiety, has been accomplished. The synthetic improvement from previous synthetic conditions facilitated our gram-scale synthesis of the chiral octalin that possesses seven stereogenic centers and that is the core skeleton of almost all of the tanzawaic acid family., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)
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- 2023
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34. Manipulation of an electron by photoirradiation in the electron-catalyzed cross-coupling reaction.
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Shirakawa E, Ota Y, Yonekura K, Okura K, Mizusawa S, Sarkar SK, and Abe M
- Abstract
An electron has recently been shown to catalyze the cross-coupling reaction of organometallic compounds with aryl halides. In terms of green and sustainable chemistry, the electron catalysis is much more desirable than the inevitably used transition metal catalysis but a high temperature of more than 100°C is required to achieve it. Here, we disclose that visible light photoirradiation accelerates the electron-catalyzed reaction of arylzinc reagents with aryl halides with the aid of a photoredox catalysis. Photoexcitation of a photoredox catalyst and an anion radical intermediate respectively affects the supply and transfer of the electron catalyst, promoting the cross-coupling reaction to proceed at room temperature. The supply of the electron catalyst by the photoredox catalysis makes the scope of aryl halides wider.
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- 2023
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35. Clinical characteristics of patients with psoriasis with family history: A multicenter observational study.
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Ohata C, Anezaki H, Kaneko S, Okazaki F, Ito K, Matsuzaka Y, Kikuchi S, Koike Y, Murota H, Miyagi T, Takahashi K, Sugita K, Hashimoto A, Nakahara T, Morizane S, Ohyama B, Saruwatari H, Yanase T, Yoshida Y, Yonekura K, Higashi Y, Hatano Y, Saito K, Katayama E, Yamane M, Yamazaki F, Tsuruta N, and Imafuku S
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- Humans, Medical History Taking, Japan epidemiology, Arthritis, Psoriatic diagnosis, Arthritis, Psoriatic epidemiology, Arthritis, Psoriatic genetics, Psoriasis diagnosis, Psoriasis epidemiology, Psoriasis genetics
- Abstract
Previous studies on family history of psoriasis showed that patients with a family history have an earlier onset of the disease, but such studies in Japan are still limited. To elucidate the characteristics of patients with familial psoriasis, we studied the family history of patients with psoriasis using the West Japan Psoriasis Registry, a multi-institutional registry operated by 26 facilities in the western part of Japan, including university hospitals, community hospitals, and clinics. This study enrolled 1847 patients registered between September 2019 and December 2021, with 199 (10.8%) having a family history of psoriasis. Patients with a family history of psoriasis had significantly earlier onset of the disease than those without a family history. Furthermore, patients with a family history of psoriasis had significantly longer disease duration. Psoriatic arthritis (PsA) was significantly more common in patients with a family history (69/199, 34.7%) than in those without a family history (439/1648, 26.6%) (adjusted P = 0.023). A subanalysis of patients with PsA revealed a significant difference in the patient global assessment (PaGA) score in Fisher's exact test and adjusted test. The numbers of patients with PaGA 0/1 were 29 (43.3%) and 172 (39.9%) in patients with PsA with and without family history of psoriasis, respectively, whereas the numbers of patients with PaGA 3/4 were 13 (19.4%) and 145 (33.6%) in patients with PsA with and without family history of psoriasis, respectively. Other disease severity variables did not show a difference between the two groups. Our findings suggest that genetics play a larger role in the development of PsA than in the development of psoriasis vulgaris. Most cases of PsA occur in patients who already have psoriasis, therefore dermatologists should pay attention to joint symptoms, especially in patients with psoriasis who have a family history of psoriasis., (© 2023 Japanese Dermatological Association.)
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- 2023
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36. Survival rates of systemic interventions for psoriasis in the Western Japan Psoriasis Registry: A multicenter retrospective study.
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Yanase T, Tsuruta N, Yamaguchi K, Ohata C, Ohyama B, Katayama E, Sugita K, Kuwashiro M, Hashimoto A, Yonekura K, Higashi Y, Murota H, Koike Y, Matsuzaka Y, Kikuchi S, Hatano Y, Saito K, Takahashi K, Miyagi T, Kaneko S, Ota M, Harada K, Morizane S, Ikeda K, Furue M, Nakahara T, Okazaki F, Sasaki N, Okada E, Yoshida Y, Ito K, and Imafuku S
- Subjects
- Humans, Retrospective Studies, Survival Rate, Japan epidemiology, Cyclosporine therapeutic use, Registries, Arthritis, Psoriatic drug therapy, Psoriasis drug therapy, Psoriasis diagnosis, Biological Products therapeutic use
- Abstract
Psoriasis affects approximately 0.3% of the Japanese population. Recently, various effective systemic drugs have become available, and the continuation of a given treatment has become critical because of the chronic nature of psoriasis. Factors affecting drug survival (the time until treatment discontinuation) in psoriasis treatment include efficacy, safety, ease of use, and patient preference. In the present study, the authors retrospectively surveyed a multifacility patient registry to determine the real-world evidence of the survival rate of systemic interventions for psoriasis treatment. Patients with psoriasis who visited 20 facilities in the Western Japan area between January 2019 and May 2020 and gave written consent were registered as study participants, and their medical history of systemic interventions for psoriasis (starting from 2010) was retrospectively collected and analyzed. The drugs investigated were adalimumab, infliximab, ustekinumab, secukinumab, ixekizumab, brodalumab, guselkumab, risankizumab, cyclosporine, and apremilast. When drugs were discontinued, the reasons were also recorded. A total of 1003 patients with psoriasis including 268 with psoriatic arthritis (PsA) were enrolled. In biologics, more recently released drugs such as interleukin 17 inhibitors showed a numerically higher survival rate in the overall (post-2010) analysis. However, in the subset of patients who began treatment after 2017, the difference in the survival rate among the drugs was smaller. The reasons for discontinuing drugs varied, but a loss of efficacy against dermatological or joint symptoms were relatively frequently seen with some biologics and cyclosporine. The stratification of drug survival rates based on patient characteristics such as bio-naive or experienced, normal weight or obese, and with or without PsA, revealed that bio-experienced, obese, and PsA groups had poorer survival rates for most drugs. No notable safety issues were identified in this study. Overall, the present study revealed that the biologics show differences in their tendency to develop a loss of efficacy, and the factors that negatively impact the survival rate of biologics include the previous use of biologics, obesity, and PsA., (© 2023 Japanese Dermatological Association.)
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- 2023
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37. Prevalence of human T-lymphotropic virus type I in patients with psoriasis and its effect on treatment choice: A multicenter observational study.
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Yonekura K, Tsuruta N, Miyagi T, Koike Y, Higashi Y, Nakahara T, Ohata C, Kaneko S, Yamaguchi M, Saito K, Yanase T, and Imafuku S
- Subjects
- Humans, Prevalence, Human T-lymphotropic virus 1, Psoriasis drug therapy, Psoriasis epidemiology, HTLV-I Infections complications, HTLV-I Infections epidemiology
- Abstract
Competing Interests: Conflict of interest Sakae Kaneko received honoraria from Eli Lilly Japan. Other authors have no conflict of interest to declare.
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- 2023
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38. Measurement of charges and chemical bonding in a cryo-EM structure.
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Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, and Yonekura K
- Abstract
Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths., (© 2023. The Author(s).)
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- 2023
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39. Landscape of immunoglobulin heavy chain γ gene class switch recombination in patients with adult T-cell leukemia-lymphoma.
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Hiramatsu H, Nosaka K, Kusumoto S, Nakano N, Choi I, Yoshimitsu M, Imaizumi Y, Hidaka M, Sasaki H, Makiyama J, Ohtsuka E, Jo T, Ogata M, Ito A, Yonekura K, Tatetsu H, Kato T, Kawakita T, Suehiro Y, Ishitsuka K, Iida S, Matsutani T, Nishikawa H, Utsunomiya A, Ueda R, and Ishida T
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- Humans, Immunoglobulin Class Switching genetics, Immunoglobulin Heavy Chains genetics, Immunoglobulin gamma-Chains genetics, Gene Rearrangement, B-Lymphocyte, Heavy Chain, Leukemia-Lymphoma, Adult T-Cell genetics
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- 2023
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40. Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography.
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Takaba K, Maki-Yonekura S, Inoue I, Tono K, Hamaguchi T, Kawakami K, Naitow H, Ishikawa T, Yabashi M, and Yonekura K
- Abstract
Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)
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- 2023
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41. An open-label, single-arm phase 2 trial of valemetostat for relapsed or refractory adult T-cell leukemia/lymphoma.
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Izutsu K, Makita S, Nosaka K, Yoshimitsu M, Utsunomiya A, Kusumoto S, Morishima S, Tsukasaki K, Kawamata T, Ono T, Rai S, Katsuya H, Ishikawa J, Yamada H, Kato K, Tachibana M, Kakurai Y, Adachi N, Tobinai K, Yonekura K, and Ishitsuka K
- Subjects
- Adult, Humans, Aged, Recurrence, Enzyme Inhibitors, Chronic Disease, Leukemia-Lymphoma, Adult T-Cell drug therapy, Lymphoma, Neutropenia, Lymphopenia, Thrombocytopenia
- Abstract
Adult T-cell leukemia/lymphoma (ATL) is an aggressive non-Hodgkin lymphoma with poor prognosis and few treatment options for patients with relapsed, recurrent, or refractory disease. We evaluated the efficacy and safety of valemetostat, a potent enhancer of zeste homolog 2 (EZH2) and EZH1 inhibitor, in treating relapsed or refractory (R/R) ATL. This multicenter phase 2 trial enrolled patients with R/R aggressive ATL (acute, lymphoma, unfavorable chronic type). Patients received valemetostat 200 mg/day orally until progressive disease or unacceptable toxicity. The primary end point was overall response rate (ORR) centrally assessed by an independent efficacy assessment committee (IEAC). Secondary end points included best response in disease compartments, duration of response (DOR), pharmacokinetics, and safety. Twenty-five patients (median age, 69.0 years) with a median of 3 prior lines of therapy were enrolled; 24 had prior mogamulizumab treatment. The primary end point was met with a centrally reviewed ORR of 48.0% (90% confidence interval [CI], 30.5-65.9), including 5 complete and 7 partial remissions. Patients pretreated with mogamulizumab had an ORR of 45.8% (4 complete and 7 partial remissions). IEAC-assessed median DOR was not reached (NR) (95% CI, 1.87 to NR; months). Treatment-emergent adverse events (TEAEs) were manageable. TEAEs that occurred in ≥20% of patients included thrombocytopenia, anemia, alopecia, dysgeusia, neutropenia, lymphopenia, leukopenia, decreased appetite, and pyrexia. Grade ≥3 TEAEs included thrombocytopenia, anemia, lymphopenia, leukopenia, and neutropenia. Valemetostat demonstrated promising efficacy and tolerability in heavily pretreated patients, warranting further investigation in treating R/R ATL. This trial was registered at www.clinicaltrials.gov as #NCT04102150., (© 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)
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- 2023
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42. Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins.
- Author
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Himiyama T, Hamaguchi T, Yonekura K, and Nakamura T
- Abstract
In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from Thermococcus kodakaraensis , which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations.
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- 2023
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43. Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.
- Author
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Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, and Shen JR
- Subjects
- Animals, Iron, Photosystem I Protein Complex genetics, Cryoelectron Microscopy, Anabaena genetics, Copepoda
- Abstract
Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs., (© 2023. The Author(s).)
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- 2023
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44. [A Case of Recurrent Breast Cancer with Multiple Bone Metastasis Effectively Treated by CDK4/6 Inhibitor in Addition to Aromatase Inhibitor].
- Author
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Satoh E, Hara M, Uehira D, Yonekura K, Murakata A, Ohinata R, Toyofuku Y, Tanami H, Osanai T, Sugano N, and Sakoma T
- Subjects
- Humans, Female, Middle Aged, Aromatase Inhibitors therapeutic use, Letrozole, Mastectomy, Lymph Node Excision, Cyclin-Dependent Kinase 4, Breast Neoplasms drug therapy, Breast Neoplasms surgery, Breast Neoplasms pathology
- Abstract
We report a case of recurrent breast cancer with multiple bone metastasis in a 62-year-old woman. Her breast cancer (invasive ductal carcinoma, T2N0M0, Stage ⅡA)was resected in 2001(partial mastectomy plus axillary lymph node dissection) with adjuvant chemotherapy(UFT)and irradiation to her left remnant breast. In February 2018, she complained of severe pain in right femoral joint and hip. CT scan showed a left cystic breast tumor(17 cm)and multiple bone metastasis. The core needle biopsy of the costal bone lesion and left mastectomy were performed. These pathological findings were recurrence of the breast cancer(ER+). The endocrine therapy(exemestane, aromatase inhibitor), the administration of denosumab and irradiation to painful bone lesions were performed, but it did not suppress tumor progression. The treatment of letrozole plus palbociclib(CDK4/6 inhibitor)were continued for 3 months from May 2018, and this therapy made her bone lesions smaller, but palbociclib were stopped due to its severe neutropenia. After that, the single administration of letrozole was continued, but the tumor marker did not become normal. In February 2019, abemaciclib was administered in addition to letrozole. One year later, her symptoms improved and her bone metastases have showed partial response.
- Published
- 2022
45. CCR7 alterations associated with inferior outcome of adult T-cell leukemia/lymphoma under mogamulizumab treatment.
- Author
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Sakamoto Y, Ishida T, Masaki A, Murase T, Ohtsuka E, Takeshita M, Muto R, Iwasaki H, Ito A, Kusumoto S, Nakano N, Tokunaga M, Yonekura K, Tashiro Y, Iida S, Utsunomiya A, Ueda R, and Inagaki H
- Subjects
- Humans, Leukemia-Lymphoma, Adult T-Cell drug therapy, Leukemia-Lymphoma, Adult T-Cell genetics, Receptors, CCR7 genetics, Antibodies, Monoclonal, Humanized therapeutic use
- Abstract
Adult T-cell leukemia/lymphoma (ATL) patients have a very poor prognosis. The humanized anti-CCR4 therapeutic monoclonal antibody, mogamulizumab, is a key agent for ATL treatment. Our previous integrated molecular analysis demonstrated that among all the driver genes in ATL, CCR7 gene alterations were significantly associated with clinical response to mogamulizumab. Accordingly, here we investigated the detailed clinical impact of CCR7 alterations in a larger cohort of ATL patients. These CCR7 alterations, most of which lead to C-terminus truncations, were observed in 27 of 223 patients (12%). For patients receiving mogamulizumab but not allogeneic hematopoietic stem cell transplantation (HSCT), CCR7 alterations were significantly associated with worse survival (median survival from the first dose of mogamulizumab of 0.7 years for 12 patients with CCR7 alterations vs. 1.6 years for 72 patients without, p = 0.020). On the other hand, the presence or absence of CCR7 alterations had no significant impact on survival in the entire cohort (median overall survival of 1.4 and 1.8 years, respectively, p = 0.901), or on the survival of patients receiving allogeneic HSCT (median survival from the day of transplantation of 0.9 years for 6 patients with CCR7 alterations and 1.4 years for 48 without, p = 0.543). Multivariate analysis indicated that patients with CCR4 alterations but lacking CCR7 alterations (n = 20) had significantly better survival after receiving mogamulizumab-containing treatments (hazard ratio for survival, 0.437, 95% confidence interval, 0.192-0.994). This study contributes to the establishment of precision medicine for ATL., (© 2022 The Authors. Hematological Oncology published by John Wiley & Sons Ltd.)
- Published
- 2022
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46. ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.
- Author
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Sekiyama N, Takaba K, Maki-Yonekura S, Akagi KI, Ohtani Y, Imamura K, Terakawa T, Yamashita K, Inaoka D, Yonekura K, Kodama TS, and Tochio H
- Subjects
- Distal Myopathies genetics, Distal Myopathies metabolism, Humans, Mutation, Protein Conformation, beta-Strand genetics, Protein Domains genetics, Amino Acids chemistry, Amino Acids genetics, Amyotrophic Lateral Sclerosis genetics, Amyotrophic Lateral Sclerosis metabolism, Prions chemistry, Protein Aggregation, Pathological genetics, T-Cell Intracellular Antigen-1 chemistry, T-Cell Intracellular Antigen-1 genetics
- Abstract
T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing β-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.
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- 2022
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47. Oral histone deacetylase inhibitor tucidinostat (HBI-8000) in patients with relapsed or refractory adult T-cell leukemia/lymphoma: Phase IIb results.
- Author
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Utsunomiya A, Izutsu K, Jo T, Yoshida S, Tsukasaki K, Ando K, Choi I, Imaizumi Y, Kato K, Kurosawa M, Kusumoto S, Miyagi T, Ohtsuka E, Sasaki O, Shibayama H, Shimoda K, Takamatsu Y, Takano K, Yonekura K, Makita S, Taguchi J, Gillings M, Onogi H, and Tobinai K
- Subjects
- Adult, Benzamides, Histone Deacetylase Inhibitors adverse effects, Humans, Prospective Studies, Pyridines, Recurrence, Treatment Outcome, Leukemia-Lymphoma, Adult T-Cell drug therapy, Lymphoma, Follicular drug therapy
- Abstract
This multicenter, prospective phase IIb trial evaluating the efficacy and safety of tucidinostat (HBI-8000) in patients with relapsed or refractory (R/R) adult T-cell leukemia/lymphoma (ATLL) was undertaken in Japan. Eligible patients had R/R ATLL and had failed standard of care treatment with chemotherapy and with mogamulizumab. Twenty-three patients received tucidinostat 40 mg orally twice per week and were included in efficacy and safety analyses. The primary end-point was objective response rate (ORR) assessed by an independent committee. The ORR was 30.4% (95% confidence interval [CI], 13.2, 52.9]. Median progression-free survival was 1.7 months (95% CI, 0.8, 7.4), median duration of response was 9.2 months (95% CI, 2.6, not reached), and median overall survival was 7.9 months (95% CI, 2.3, 18.0). All patients experienced adverse events (AEs), which were predominantly hematologic and gastrointestinal. Incidence of grade 3 or higher AEs was 78.3%; most were laboratory abnormalities (decreases in platelets, neutrophils, white blood cells, and hemoglobin). Tucidinostat was well tolerated with AEs that could be mostly managed with supportive care and dose modifications. Tucidinostat is a meaningful treatment option for R/R ATLL patients; further investigation is warranted., (© 2022 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)
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- 2022
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48. Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
- Author
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Kawakami K, Hamaguchi T, Hirose Y, Kosumi D, Miyata M, Kamiya N, and Yonekura K
- Subjects
- Cryoelectron Microscopy, Energy Transfer, Light-Harvesting Protein Complexes metabolism, Phycobilisomes metabolism, Cyanobacteria metabolism, Rhodophyta metabolism
- Abstract
Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
49. Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange.
- Author
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Kimura A, Kitoh-Nishioka H, Aota T, Hamaguchi T, Yonekura K, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Ifuku K, Yamashita E, Kashino Y, and Itoh S
- Subjects
- Chlorophyll chemistry, Chlorophyll A, Light, Models, Theoretical, Photosystem II Protein Complex chemistry, Cyanobacteria metabolism, Photosystem I Protein Complex chemistry
- Abstract
A theoretical model of the far-red-light-adapted photosystem I (PSI) reaction center (RC) complex of a cyanobacterium, Acaryochloris marina (AmPSI), was constructed based on the exciton theory and the recently identified molecular structure of AmPSI by Hamaguchi et al. ( Nat. Commun. , 2021 , 12 , 2333). A. marina performs photosynthesis under the visible to far-red light (400-750 nm), which is absorbed by chlorophyll d (Chl- d ). It is in contrast to the situation of all the other oxygenic photosynthetic processes of cyanobacteria and plants, which contains chlorophyll a (Chl- a ) that absorbs only 400-700 nm visible light. AmPSI contains 70 Chl- d , 1 Chl- d
' , 2 pheophytin a (Pheo- a ), and 12 carotenoids in the currently available structure. A special pair of Chl- d /Chl- d' acts as the electron donor (P740) and two Pheo- a act as the primary electron acceptor A0 as the counterparts of P700 and Chl- a , respectively, of Chl- a -type PSIs. The exciton Hamiltonian of AmPSI was constructed considering the excitonic coupling strength and site energy shift of individual pigments using the Poisson-TrESP (P-TrESP) and charge density coupling (CDC) methods. The model was constructed to fit the experimentally measured spectra of absorption and circular dichroism (CD) spectra during downhill/uphill excitation energy transfer processes. The constructed theoretical model of AmPSI was further compared with the Chl- a -type PSI of Thermosynechococcus elongatus (TePSI), which contains only Chl- a and Chl- a' . The functional properties of AmPSI and TePSI were further examined by the in silico exchange of Chl- d by Chl- a in the models.- Published
- 2022
- Full Text
- View/download PDF
50. Detection of gait variations by using artificial neural networks.
- Author
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Guzelbulut C, Shimono S, Yonekura K, and Suzuki K
- Abstract
Walking is an everyday activity and contains variations from person to person, from one step to another step. The variation may occur due to the uniqueness of each gait cycle, personal parameters, such as age, walking speed, etc., and the existence of a gait abnormality. Understanding the normal variation depending on personal parameters helps medical experts to identify deviations from normal gait and engineers to design compatible orthotic and prosthetic products. In the present study, we aimed to obtain normal gait variations based on age, sex, height, weight, and walking speed. For this purpose, a large dataset of walking trials was used to model normal walking. An artificial neural network-based gait characterization model is proposed to show the relation between personal parameters and gait parameters. The neural network model simulates normal walking by considering the effect of personal parameters. The predicted behavior of gait parameters by artificial neural network model has a similarity with existing literature. The differences between experimental data and the neural network model were calculated. To determine how much deviation between predictions and experiments can be considered excessive, the distributions of differences for each gait parameter were obtained. The phases of walking in which excessive differences were intensified were determined. It was revealed that the artificial neural network-based gait characterization model exhibits the behavior of the normal gait parameters depending on the personal parameters., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© Korean Society of Medical and Biological Engineering 2022.)
- Published
- 2022
- Full Text
- View/download PDF
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