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Sakabe T, Shimomura S, Ogura Y, Okubo KI, Yamashita H, Suzuki H, Tanida J. Spatial-photonic Ising machine by space-division multiplexing with physically tunable coefficients of a multi-component model. Opt Express 2023; 31:44127-44138. [PMID: 38178491 DOI: 10.1364/oe.508069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
This paper proposes a space-division multiplexed spatial-photonic Ising machine (SDM-SPIM) that physically calculates the weighted sum of the Ising Hamiltonians for individual components in a multi-component model. Space-division multiplexing enables tuning a set of weight coefficients as an optical parameter and obtaining the desired Ising Hamiltonian at a time. We solved knapsack problems to verify the system's validity, demonstrating that optical parameters impact the search property. We also investigated a new dynamic coefficient search algorithm to enhance search performance. The SDM-SPIM would physically calculate the Hamiltonian and a part of the optimization with an electronics process.
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Yamashita H, Okubo KI, Shimomura S, Ogura Y, Tanida J, Suzuki H. Low-Rank Combinatorial Optimization and Statistical Learning by Spatial Photonic Ising Machine. Phys Rev Lett 2023; 131:063801. [PMID: 37625069 DOI: 10.1103/physrevlett.131.063801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 08/27/2023]
Abstract
The spatial photonic Ising machine (SPIM) [13D. Pierangeli et al., Large-Scale Photonic Ising Machine by Spatial Light Modulation, Phys. Rev. Lett. 122, 213902 (2019).PRLTAO0031-900710.1103/PhysRevLett.122.213902] is a promising optical architecture utilizing spatial light modulation for solving large-scale combinatorial optimization problems efficiently. The primitive version of the SPIM, however, can accommodate Ising problems with only rank-one interaction matrices. In this Letter, we propose a new computing model for the SPIM that can accommodate any Ising problem without changing its optical implementation. The proposed model is particularly efficient for Ising problems with low-rank interaction matrices, such as knapsack problems. Moreover, it acquires the learning ability of Boltzmann machines. We demonstrate that learning, classification, and sampling of the MNIST handwritten digit images are achieved efficiently using the model with low-rank interactions. Thus, the proposed model exhibits higher practical applicability to various problems of combinatorial optimization and statistical learning, without losing the scalability inherent in the SPIM architecture.
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Affiliation(s)
- Hiroshi Yamashita
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Ken-Ichi Okubo
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Suguru Shimomura
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Yusuke Ogura
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Jun Tanida
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Hideyuki Suzuki
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
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Okubo KI, Umeno K. Infinite ergodicity that preserves the Lebesgue measure. Chaos 2021; 31:033135. [PMID: 33810722 DOI: 10.1063/5.0029751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
In this study, we prove that a countably infinite number of one-parameterized one-dimensional dynamical systems preserve the Lebesgue measure and are ergodic for the measure. The systems we consider connect the parameter region in which dynamical systems are exact and the one in which almost all orbits diverge to infinity and correspond to the critical points of the parameter in which weak chaos tends to occur (the Lyapunov exponent converging to zero). These results are a generalization of the work by Adler and Weiss. Using numerical simulation, we show that the distributions of the normalized Lyapunov exponent for these systems obey the Mittag-Leffler distribution of order 1/2.
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Affiliation(s)
- Ken-Ichi Okubo
- Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ken Umeno
- Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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Seto K, Masago K, Fujita S, Haneda M, Horio Y, Hida T, Kuroda H, Hosoda W, Okubo KI. Targeted RNA sequencing with touch imprint cytology samples for non-small cell lung cancer patients. Thorac Cancer 2020; 11:1827-1834. [PMID: 32372482 PMCID: PMC7327906 DOI: 10.1111/1759-7714.13460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 01/04/2023] Open
Abstract
Background RNA‐based sequencing is considered ideal for detecting pathogenic fusion‐genes compared to DNA‐based assays and provides valuable information about the relative expression of driver genes. However, RNA from formalin‐fixed paraffin‐embedded tissue has issues with both quantity and quality, making RNA‐based sequencing difficult in clinical practice. Analyzing stamp‐derived RNA with next‐generation sequencing (NGS) can address the above‐mentioned obstacles. In this study, we validated the analytical specifications and clinical performance of our custom panel for RNA‐based assays on the Ion Torrent platform. Methods To evaluate our custom RNA lung panel, we first examined the gene sequences of RNA derived from 35 NSCLC tissues with diverse backgrounds by conventional methods and NGS. Next, we moved to the clinical phase, where clinical samples (all stamp‐derived RNA) were used to examine variants. In the clinical phase we conducted an NGS analysis while simultaneously applying conventional approaches to assess the feasibility and validity of the panel in clinical practice. Results In the prerun phase, all of the variants confirmed with conventional methods were detected by NGS. In the clinical phase, a total of 80 patients were enrolled and 80 tumor specimens were sequenced from February 2018 to December 2018. There were 66 cases in which the RNA concentration was too low to be measured, but sequencing was successful in the vast majority of cases. The concordance between NGS and conventional methods was 95.0%. Conclusions RNA extraction using stamp specimens and panel sequencing by NGS were considered applicable in clinical settings. Key points Significant findings of the study Next‐generation sequencing using RNA from stamp specimens was able to detect driver gene changes in non‐small cell lung cancer including fusion genes with the same accuracy as conventional methods. What this study adds Using RNA from stamp specimens obtained from biopsy increases the number of candidate cases for RNA sequencing in clinical settings.
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Affiliation(s)
- Katsutoshi Seto
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Shiro Fujita
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Masataka Haneda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | | | - Toyoaki Hida
- Thoracic Oncology, Aichi Cancer Center, Nagoya, Japan
| | | | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Ken-Ichi Okubo
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
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Singh RP, Okubo KI, Ohtani K, Adachi K, Sonomoto K, Nakayama J. Rationale design of quorum-quenching peptides that target the VirSR system of Clostridium perfringens. FEMS Microbiol Lett 2015; 362:fnv188. [PMID: 26443835 DOI: 10.1093/femsle/fnv188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2015] [Indexed: 11/13/2022] Open
Abstract
In Clostridium perfringens, a 5-membered thiolactone peptide acts as an autoinducing peptide (AIPCp) to activate the VirSR two-component signal transduction system, which in turn controls the expression of genes encoding multiple toxins, including α, θ and κ. To develop anti-pathogenic agents against virulent C. perfringens, quorum-quenching peptides were rationally designed based on the structure-activity relationship (SAR) data on AIPCp. Alanine scanning study of AIPCp suggested that Trp(3) and Phe(4) are involved in receptor binding and activation, respectively. On the basis of the SAR, we designed two quorum-quenching peptides with different modes of action: Z-AIPCp-L2A/T5A (partial agonist) and Z-AIPCp-F4A/T5S (partial antagonist). Both peptides significantly attenuated transcription of θ toxin gene (pfoA) in a virulent strain of C. perfringens with IC50 = 0.32 and 0.72 μM, respectively.
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Affiliation(s)
- Ravindra Pal Singh
- Laboratory of Microbial Technology, Department of Biochemistry and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Ken-Ichi Okubo
- Laboratory of Microbial Technology, Department of Biochemistry and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Kaori Ohtani
- Department of Bacteriology, University of Kanazawa, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8203, Japan
| | - Keika Adachi
- Laboratory of Microbial Technology, Department of Biochemistry and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Department of Biochemistry and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan Laboratory of Functional Food Design, Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Department of Biochemistry and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
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Desouky SE, Shojima A, Singh RP, Matsufuji T, Igarashi Y, Suzuki T, Yamagaki T, Okubo KI, Ohtani K, Sonomoto K, Nakayama J. Cyclodepsipeptides produced by actinomycetes inhibit cyclic-peptide-mediated quorum sensing in Gram-positive bacteria. FEMS Microbiol Lett 2015; 362:fnv109. [PMID: 26149266 DOI: 10.1093/femsle/fnv109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 12/18/2022] Open
Abstract
Cyclic peptides are commonly used as quorum-sensing autoinducers in Gram-positive Firmicutes bacteria. Well-studied examples of such molecules are thiolactone and lactone, used to regulate the expression of a series of virulence genes in the agr system of Staphylococcus aureus and the fsr system of Enterococcus faecalis, respectively. Three cyclodepsipeptides WS9326A, WS9326B and cochinmicin II/III were identified as a result of screening actinomycetes culture extracts for activity against the agr/fsr system. These molecules are already known as receptor antagonists, the first two for tachykinin and the last one for endothelin. WS9326A also inhibited the transcription of pfoA regulated by the VirSR two-component system in Clostridium perfringens. Receptor-binding assays using a fluorescence-labeled autoinducer (FITC-GBAP) showed that WS9326A and WS9326B act as receptor antagonists in this system. In addition, an ex vivo assay showed that WS9326B substantially attenuated the toxicity of S. aureus for human corneal epithelial cells. These results suggest that these three natural cyclodepsipeptides have therapeutic potential for targeting the cyclic peptide-mediated quorum sensing of Gram-positive pathogens.
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Affiliation(s)
- Said E Desouky
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Department of Botany and Microbiology, Faculty of Science, Al-azhar University, 11884 Nasr, Cairo, Egypt
| | - Akane Shojima
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Ravindra Pal Singh
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takahisa Matsufuji
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takashi Suzuki
- Department of Ophthalmology, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Tohru Yamagaki
- Suntory Foundation for Life Sciences, Bioorganic Research Institute, 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Ken-Ichi Okubo
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kaori Ohtani
- Department of Bacteriology, University of Kanazawa, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8203, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Laboratory of Functional Food Design, Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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