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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

5. 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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8. 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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10. 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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11. 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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14. 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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16. 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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17. 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

19. 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

23. 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

24. 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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27. 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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29. Molecular properties of a DTD channelrhodopsin from Guillardia theta

Author

Yamauchi, Yumeka, Konno, Masae, Ito, Shota, Tsunoda, Satoshi P., Inoue, Keiichi, and Kandori, Hideki

Subjects
flash photolysis, light-gated channel, light-induced difference FTIR spectra, Regular Article, microbial rhodopsin, patch clamp
Abstract

Microbial rhodopsins are membrane proteins found widely in archaea, eubacteria and eukaryotes (fungal and algal species). They have various functions, such as light-driven ion pumps, light-gated ion channels, light sensors and light-activated enzymes. A light-driven proton pump bacteriorhodopsin (BR) contains a DTD motif at positions 85, 89, and 96, which is unique to archaeal proton pumps. Recently, channelrhodopsins (ChRs) containing the DTD motif, whose sequential identity is ~20% similar to BR and to cation ChRs in Chlamydomonas reinhardtii (CrCCRs), were found. While extensive studies on ChRs have been performed with CrCCR2, the molecular properties of DTD ChRs remain an intrigue. In this paper, we studied a DTD rhodopsin from G. theta (GtCCR4) using electrophysiological measurements, flash photolysis, and low-temperature difference FTIR spectroscopy. Electrophysiological measurements clearly showed that GtCCR4 functions as a light-gated cation channel, similar to other G. theta DTD ChRs (GtCCR1-3). Light-driven proton pump activity was also suggested for GtCCR4. Both electrophysiological and flash photolysis experiments showed that channel closing occurs upon reprotonation of the Schiff base, suggesting that the dynamics of retinal and channels are tightly coupled in GtCCR4. From Fourier transform infrared (FTIR) spectroscopy at 77 K, we found that the primary reaction is an all-trans to a 13-cis photoisomerization, like other microbial rhodopsins, although perturbations in the secondary structure were much smaller in GtCCR4 than in CrCCR2.

Published
2017

30. Utilizing of Monitor of Package Tour for Tourism

Author

Ito, Shota and Kawahara, Susumu

Abstract

本研究は、近年多く用いられてきている「モニターツアー」の全体像と地域振興に資する活用方法を明らかにすることを目的とする。過去に催行されたモニターツアーを対象として調査を行い目的別に類型化した結果「地域資源発掘・評価」「旅行商品開発検証」「地域PR」の３タイプが主流となっていることを明らかにした。とりわけ下呂市では、参加者提案タイプや定量調査との併用といった戦略性ある独創的なモニターツアーの催行により、受入体制の構築や新たな戦略づくりにモニターツアーが貢献していることが分かった。総括として、モニターツアーを催行するまでの要点をまとめ、地域の観光振興施策に対応したモニターツアーのあり方を示した。

Published
2015

34. A natural light-driven inward proton pump

Author

Inoue, Keiichi, primary, Ito, Shota, additional, Kato, Yoshitaka, additional, Nomura, Yurika, additional, Shibata, Mikihiro, additional, Uchihashi, Takayuki, additional, Tsunoda, Satoshi P., additional, and Kandori, Hideki, additional

Published
2016
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35. Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution

Author

Ito, Shota, Iwaki, Masayo, Sugita, Shinya, Abe-Yoshizumi, Rei, Iwata, Tatsuya, Inoue, Keiichi, and Kandori, Hideki

Abstract

Protein function is coupled to its structural changes, for which stimulus-induced difference Fourier-transform infrared (FTIR) spectroscopy is a powerful method. By optimizing the attenuated total reflection (ATR)-FTIR analysis on sodium-pumping rhodopsin KR2 in aqueous solution, we first measured the accurate difference spectra upon sodium binding in the whole IR region (4000–1000 cm–1). The new spectral window allows the analysis of not only the fingerprint region (1800–1000 cm–1) but also the hydrogen-bonding donor region (4000–1800 cm–1), revealing an unusually strong hydrogen bond of Tyr located in the sodium binding site of KR2. Progress in ATR-FTIR difference spectroscopy provides an approach to investigating stimulus-induced structural changes of membrane proteins under physiological aqueous conditions.

Published
2024
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38. Extraction of Resveratrol from Melinjo (Gnetum gnemon L.) Seeds Using Mixtures of Liquid Carbon Dioxide and Ethanol

Author

MISHIMA, Kenji, primary, SIREGAR, Yusraini Dian Inayati, additional, KAWAMURA, Hirofumi, additional, KAWAKAMI, Ryo, additional, ITO, Shota, additional, INOUE, Yuuta, additional, HIROTA, Tetsuya, additional, HARADA, Takunori, additional, KATO, Takafumi, additional, MISUMI, Makoto, additional, SUETSUGU, Tadashi, additional, IRIE, Keiichi, additional, MISHIMA, Kenichi, additional, MUSTOFA, Salim, additional, HASANAH, Fauziyah, additional, ZAHARO, Hilyatuz, additional, PUTRI, Lily Surayya Eka, additional, and SALIM, Agus, additional

Published
2015
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39. Extraction of Apigenin and Luteolin from Leaves of Alfalfa (Medicago sativa L.) Using Mixtures of Liquid Carbon Dioxide and Ethanol

Author

MISHIMA, Kenji, primary, KAWAMURA, Hirofumi, additional, KAWAKAMI, Ryo, additional, ITO, Shota, additional, INOUE, Yuuta, additional, HIROTA, Tetsuya, additional, HARADA, Takunori, additional, KATO, Takafumi, additional, SHARMIN, Tanjina, additional, MISUMI, Makoto, additional, SUETSUGU, Tadashi, additional, IRIE, Keiichi, additional, MISHIMA, Kenichi, additional, MUSTOFA, Salim, additional, HASANAH, Fauziyah, additional, SIREGAR, Yusraini Dian Inayati, additional, ZAHARO, Hilyatuz, additional, PUTRI, Lily Surayya Eka, additional, and SALIM, Agus, additional

Published
2015
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40. Liquid Carbon Dioxide Extraction of Xanthones from the Pericarps of Garcinia Mangostana Linn. Enhanced by Ultrasonic Irradiation

Author

MISHIMA, Kenji, primary, KAWAMURA, Hirofumi, additional, ITO, Shota, additional, INOUE, Yuuta, additional, HIROTA, Tetsuya, additional, KATO, Takafumi, additional, SHARMIN, Tanjina, additional, KAWAKAMI, Ryo, additional, IRIE, Keiichi, additional, MISHIMA, Kenichi, additional, HARADA, Takunori, additional, MUSTOFA, Salim, additional, HASANAH, Fauziyah, additional, SIREGAR, Yusraini Dian Inayati, additional, PUTRI, Lily Surayya Eka, additional, and SALIM, Agus, additional

Published
2015
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