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2. OpenLB User Guide: Associated with Release 1.6 of the Code

Author

Kummerländer, Adrian, Avis, Samuel J., Kusumaatmaja, Halim, Bukreev, Fedor, Crocoll, Michael, Dapelo, Davide, Großmann, Simon, Hafen, Nicolas, Ito, Shota, Jeßberger, Julius, Kummer, Eliane, Marquardt, Jan E., Mödl, Johanna, Pertzel, Tim, Prinz, František, Raichle, Florian, Sadric, Martin, Schecher, Maximilian, Teutscher, Dennis, Simonis, Stephan, and Krause, Mathias J.

Subjects
Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, Mathematics - Numerical Analysis, 97N80, 74S30, 76M25, 80M25, 82C80, G.4
Abstract

OpenLB is an object-oriented implementation of LBM. It is the first implementation of a generic platform for LBM programming, which is shared with the open source community (GPLv2). Since the first release in 2007, the code has been continuously improved and extended which is documented by thirteen releases as well as the corresponding release notes which are available on the OpenLB website (https://www.openlb.net). The OpenLB code is written in C++ and is used by application programmers as well as developers, with the ability to implement custom models OpenLB supports complex data structures that allow simulations in complex geometries and parallel execution using MPI, OpenMP and CUDA on high-performance computers. The source code uses the concepts of interfaces and templates, so that efficient, direct and intuitive implementations of the LBM become possible. The efficiency and scalability has been checked and proved by code reviews. This user manual and a source code documentation by DoxyGen are available on the OpenLB project website.

Published
2023

9. Surgical Orthodontic Treatment for Skeletal Maxillary Protrusion in Sturge-Weber Syndrome: A Case Report and Review of the Literature

Author

Kado, Isamu, primary, Ogashira, Shintaro, additional, Ono, Shigehiro, additional, Koizumi, Koichi, additional, Nakagawa, Takayuki, additional, Yoshimi, Yuki, additional, Kunimatsu, Ryo, additional, Ito, Shota, additional, Koizumi, Yuma, additional, Ogasawara, Tomohiro, additional, Aikawa, Tomonao, additional, and Tanimoto, Kotaro, additional

Published
2024
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15. The expression of MIR125B transcripts and bone phenotypes in Mir125b2-deficient mice.

Author

Ogasawara, Tomohiro, Ito, Shota, Ogashira, Shintaro, Hoshino, Tomonori, Sotomaru, Yusuke, Yoshiko, Yuji, and Tanimoto, Kotaro

Subjects
*CALVARIA, *MESENCHYMAL stem cells, *PHENOTYPES, *MICE
Abstract

MIR125B, particularly its 5p strand, is apparently involved in multiple cellular processes, including osteoblastogenesis and osteoclastogenesis. Given that MIR125B is transcribed from the loci Mir125b1 and Mir125b2, three mature transcripts (MIR125B-5p, MIR125B1-3p, and MIR125B2-3p) are generated (MIR125B-5p is common to both); however, their expression profiles and roles in the bones remain poorly understood. Both primary and mature MIR125B transcripts were differentially expressed in various organs, tissues, and cells, and their expression patterns did not necessarily correlate in wild-type (WT) mice. We generated Mir125b2 knockout (KO) mice to examine the contribution of Mir125b2 to MIR125B expression profiles and bone phenotypes. Mir125b2 KO mice were born and grew normally without any changes in bone parameters. Interestingly, in WT and Mir125b2 KO, MIR125B-5p was abundant in the calvaria and bone marrow stromal cells. These results indicate that the genetic ablation of Mir125b2 does not impinge on the bones of mice, attracting greater attention to MIR125B-5p derived from Mir125b1. Future studies should investigate the conditional deletion of Mir125b1 and both Mir125b1 and Mir125b2 in mice. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Abstract 14608: Prognostic Value of Diuretic Resistance in Patients Admitted for Acute Decompensated Heart Failure With Reduced, Mid-range, or Preserved Left Ventricular Ejection Fraction

Author

Kimura, Takanari, Yamada, Takahisa, Watanabe, Tetsuya, Morita, Takashi, Furukawa, Yoshio, Tamaki, Shunsuke, Kawasaki, Masato, Kikuchi, Atsushi, Kawai, Tsutomu, Seo, Masahiro, Nakamura, Jun, Kayama, Kiyomi, Kawahira, Masatsugu, Ueda, Kunpei, Sakamoto, Daisuke, Ito, Shota, Kougame, Takehiro, Chang, Yongchol, and Fukunami, Masatake

Published
2020
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21. Crystal structure of the natural anion-conducting channelrhodopsin GtACR1

Author

Kim, Yoon Seok, Kato, Hideaki E., Yamashita, Keitaro, Ito, Shota, Inoue, Keiichi, Ramakrishnan, Charu, and Fenno, Lief E.

Subjects
Crystal structure -- Research, Rhodopsin -- Structure -- Chemical properties, Neurons, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The naturally occurring channelrhodopsin variant anion channelrhodopsin-1 (ACR1), discovered in the cryptophyte algae Guillardia theta, exhibits large light-gated anion conductance and high anion selectivity when expressed in heterologous settings, properties that support its use as an optogenetic tool to inhibit neuronal firing with light. However, molecular insight into ACR1 is lacking owing to the absence of structural information underlying light-gated anion conductance. Here we present the crystal structure of G. theta ACR1 at 2.9 Å resolution. The structure reveals unusual architectural features that span the extracellular domain, retinal-binding pocket, Schiff-base region, and anion-conduction pathway. Together with electrophysiological and spectroscopic analyses, these findings reveal the fundamental molecular basis of naturally occurring light-gated anion conductance, and provide a framework for designing the next generation of optogenetic tools.The crystal structure of anion channelrhodopsin-1 (ACR1) from the algae Guillardia theta provides insights into the basis of anion conductance., Author(s): Yoon Seok Kim [sup.1] , Hideaki E. Kato [sup.2] [sup.3] , Keitaro Yamashita [sup.4] , Shota Ito [sup.5] , Keiichi Inoue [sup.3] [sup.5] [sup.6] , Charu Ramakrishnan [sup.1] , [...]

Published
2018
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24. Image preprocessing with contrast-limited adaptive histogram equalization improves the segmentation performance of deep learning for the articular disk of the temporomandibular joint on magnetic resonance images

Author

Yoshimi, Yuki, primary, Mine, Yuichi, additional, Ito, Shota, additional, Takeda, Saori, additional, Okazaki, Shota, additional, Nakamoto, Takashi, additional, Nagasaki, Toshikazu, additional, Kakimoto, Naoya, additional, Murayama, Takeshi, additional, and Tanimoto, Kotaro, additional

Published
2023
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25. Ultrasonically enhanced extraction of luteolin and apigenin from the leaves of Perilla frutescens (L.) Britt. using liquid carbon dioxide and ethanol

Author

Kawamura, Hirofumi, Mishima, Kenji, Sharmin, Tanjina, Ito, Shota, Kawakami, Ryo, Kato, Takafumi, Misumi, Makoto, Suetsugu, Tadashi, Orii, Hideaki, Kawano, Hiroyuki, Irie, Keiichi, Sano, Kazunori, Mishima, Kenichi, Harada, Takunori, Mustofa, Salim, Hasanah, Fauziyah, Siregar, Yusraini Dian Inayati, Zahroh, Hilyatuz, Putri, Lily Surayya Eka, and Salim, Agus

Published
2016
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29. Identification of Reaction Rate Parameters from Uncertain Spatially Distributed Concentration Data Using Gradient-Based Pde Constrained Optimization

Author

Ito, Shota, primary, Jeßberger, Julius, additional, Simonis, Stephan, additional, Bukreev, Fedor, additional, Kummerländer, Adrian, additional, Zimmermann, Alexander, additional, Thäter, Gudrun, additional, Pesch, Georg, additional, Thöming, J., additional, and Krause, Mathias J., additional

Published
2023
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30. Longitudinal effects of estrogen on mandibular growth and changes in cartilage during the growth period in rats

Author

Kubo, Naoki, primary, Awada, Tetsuya, additional, Hirose, Naoto, additional, Yanoshita, Makoto, additional, Takano, Mami, additional, Nishiyama, Sayuri, additional, Tsuboi, Eri, additional, Kita, Daiki, additional, Ito, Shota, additional, Nakatani, Ayaka, additional, Onishi, Azusa, additional, Asakawa, Yuki, additional, and Tanimoto, Kotaro, additional

Published
2022
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31. Overview of Storage Batteries for Battery Electric Vehicles : Present and Future Beyond Lithium-Ion Batteries

Author

Ito, Shota and Ariyoshi, Kingo

Subjects
Battery electric vehicle, Lithium-ion battery, Next-generation batteries, Mileage per energy
Abstract

The battery electric vehicle (BEV), which uses a storage battery as a power source, requires highperformance lithium-ion batteries (LIBs) because the driving characteristics of BEV depend on battery performance. In this study, the theoretical energy density of LIBs was calculated from a scientific point of view. In addition, ...

Published
2021

34. Analysis of Electrochemical Reaction in Positive and Negative Electrodes during Capacity Recovery of Lithium Ion Battery Employing Recovery Electrodes

Author

Jun Kawaji, Ito Shota, Eiji Seki, Takefumi Okumura, Masatoshi Sugimasa, and Kohei Honkura

Subjects
Technology, Materials science, Physical and theoretical chemistry, QD450-801, Inorganic chemistry, recovery electrode, capacity recovery, Electrochemistry, Lithium-ion battery, mental disorders, Electrode, discharge curve analysis, lithium ion battery, psychological phenomena and processes
Abstract

Electrochemical reactions in positive and negative electrodes during recovery from capacity fades in lithium ion battery cells were evaluated for the purpose of revealing the recovery mechanisms. We fabricated laminated type cells with recovery electrodes, which sandwich the assemblies of negative electrodes, separators, and positive electrodes. The positive electrodes were replenished with Li+ by applying current between the recovery and the positive electrodes. A discharge curve analysis revealed that Li+ replenishment enabled the cells to recover from the capacity fade originating from capacity slippage between the positive and the negative electrodes. However, an issue is low recovery efficiency, which is defined as the ratio of recovery capacity of capacity slippage to the electric charge between the recovery and the positive electrodes. The cause of low recovery efficiency was elucidated by evaluating the positive and the negative electrodes after replenishment. It was found that the following mechanisms are involved in the replenishment of the positive electrodes: (a) Li+ are intercalated into the positive electrodes as they are released from the recovery electrodes, which significantly contributes to recovery from capacity slippage; however, (b) some amount of Li+ is released from the planes of the negative electrodes facing the positive electrodes as they are intercalated into the planes of the negative electrodes facing the recovery electrodes, which does not significantly contribute to recovery. Consequently, the recovery efficiencies were less than 50 %. We conclude that, to increase recovery efficiency, process (b) should be suppressed.

Published
2021

41. High-frequency near-infrared diode laser irradiation suppresses IL-1β-induced inflammatory cytokine expression and NF-κB signaling pathways in human primary chondrocytes

Author

Sakata, Shuzo, primary, Kunimatsu, Ryo, additional, Tsuka, Yuji, additional, Nakatani, Ayaka, additional, Gunji, Hidemi, additional, Yanoshita, Makoto, additional, Kado, Isamu, additional, Ito, Shota, additional, Putranti, Nurul Aisyah Rizky, additional, Prasetya, Rendra Chriestedy, additional, Hirose, Naoto, additional, and Tanimoto, Kotaro, additional

Published
2021
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45. Automated Segmentation of Articular Disc of the Temporomandibular Joint in Magnetic Resonance Images Using Deep Learning: A Proof-of-Concept Study

Author

Ito, Shota, primary, Mine, Yuichi, additional, Yoshimi, Yuki, additional, Takeda, Saori, additional, Tanaka, Akari, additional, Onishi, Azusa, additional, Peng, Tzu-Yu, additional, Nakamoto, Takashi, additional, Nagasaki, Toshikazu, additional, Kakimoto, Naoya, additional, Murayama, Takeshi, additional, and Tanimoto, Kotaro, additional

Published
2021
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46. Overexpression of miR-125b in Osteoblasts Improves Age-Related Changes in Bone Mass and Quality through Suppression of Osteoclast Formation

Author

Ito, Shota, Minamizaki, Tomoko, Kohno, Shohei, Sotomaru, Yusuke, Kitaura, Yoshiaki, Ohba, Shinsuke, Sugiyama, Toshie, Aubin, Jane E, Tanimoto, Kotaro, Yoshiko, Yuji, Ito, Shota, Minamizaki, Tomoko, Kohno, Shohei, Sotomaru, Yusuke, Kitaura, Yoshiaki, Ohba, Shinsuke, Sugiyama, Toshie, Aubin, Jane E, Tanimoto, Kotaro, and Yoshiko, Yuji

Abstract

We recently reported an unexpected role of osteoblast-derived matrix vesicles in the delivery of microRNAs to bone matrix. Of such microRNAs, we found that miR-125b inhibited osteoclast formation by targeting Prdm1 encoding a transcriptional repressor of anti-osteoclastogenesis factors. Transgenic (Tg) mice overexpressing miR-125b in osteoblasts by using human osteocalcin promoter grow normally but exhibit high trabecular bone mass. We have now further investigated the effects of osteoblast-mediated miR-125b overexpression on skeletal morphogenesis and remodeling during development, aging and in a situation of skeletal repair, i.e., fracture healing. There were no significant differences in the growth plate, primary spongiosa or lateral (periosteal) bone formation and mineral apposition rate between Tg and wild-type (WT) mice during early bone development. However, osteoclast number and medial (endosteal) bone resorption were less in Tg compared to WT mice, concomitant with increased trabecular bone mass. Tg mice were less susceptible to age-dependent changes in bone mass, phosphate/amide I ratio and mechanical strength. In a femoral fracture model, callus formation progressed similarly in Tg and WT mice, but callus resorption was delayed, reflecting the decreased osteoclast numbers associated with the Tg callus. These results indicate that the decreased osteoclastogenesis mediated by miR-125b overexpression in osteoblasts leads to increased bone mass and strength, while preserving bone formation and quality. They also suggest that, in spite of the fact that single miRNAs may target multiple genes, the miR-125b axis may be an attractive therapeutic target for bone loss in various age groups., T.M. was supported in part by MEXT KAKENHI (JP16K11443). Y.Y. was supported by the Raffinee International Foundation and the Ono Pharmaceutical Foundation.

Published
2021

47. Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin

Author

Oda, Kazumasa, primary, Nomura, Takashi, additional, Nakane, Takanori, additional, Yamashita, Keitaro, additional, Inoue, Keiichi, additional, Ito, Shota, additional, Vierock, Johannes, additional, Hirata, Kunio, additional, Maturana, Andrés D, additional, Katayama, Kota, additional, Ikuta, Tatsuya, additional, Ishigami, Itsuki, additional, Izume, Tamaki, additional, Umeda, Rie, additional, Eguma, Ryuun, additional, Oishi, Satomi, additional, Kasuya, Go, additional, Kato, Takafumi, additional, Kusakizako, Tsukasa, additional, Shihoya, Wataru, additional, Shimada, Hiroto, additional, Takatsuji, Tomoyuki, additional, Takemoto, Mizuki, additional, Taniguchi, Reiya, additional, Tomita, Atsuhiro, additional, Nakamura, Ryoki, additional, Fukuda, Masahiro, additional, Miyauchi, Hirotake, additional, Lee, Yongchan, additional, Nango, Eriko, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Sugahara, Michihiro, additional, Kimura, Tetsunari, additional, Shimamura, Tatsuro, additional, Fujiwara, Takaaki, additional, Yamanaka, Yasuaki, additional, Owada, Shigeki, additional, Joti, Yasumasa, additional, Tono, Kensuke, additional, Ishitani, Ryuichiro, additional, Hayashi, Shigehiko, additional, Kandori, Hideki, additional, Hegemann, Peter, additional, Iwata, So, additional, Kubo, Minoru, additional, Nishizawa, Tomohiro, additional, and Nureki, Osamu, additional

Published
2021
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50. Prognostic value of impaired hepato‐renal function and liver fibrosis in patients admitted for acute heart failure

Author

Kawahira, Masatsugu, primary, Tamaki, Shunsuke, additional, Yamada, Takahisa, additional, Watanabe, Tetsuya, additional, Morita, Takashi, additional, Furukawa, Yoshio, additional, Kawasaki, Masato, additional, Kikuchi, Atsushi, additional, Kawai, Tsutomu, additional, Seo, Masahiro, additional, Nakamura, Jun, additional, Kayama, Kiyomi, additional, Kimura, Takanari, additional, Ueda, Kunpei, additional, Sakamoto, Daisuke, additional, Kogame, Takehiro, additional, Ito, Shota, additional, Chang, Yongchol, additional, and Fukunami, Masatake, additional

Published
2021
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