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Plot data of the research paper "Optically-trapped particle tracking velocimetry" from Physical Review Fluids
No full textNumerical values of data in Figs 3, 4, 5, 6, and 8
Mesh-free perturbation source method using the closest point pair method in -eigenvalue Monte Carlo perturbation calculations
No full textIn -eigenvalue calculations using the Monte Carlo method, the perturbation source method (PSM) is a robust technique for perturbation calculations due to changes in cross sections or geometry. The PSM requires consideration of changes in the fission source distribution resulting from perturbations. Thus far, the region where the fission source exists has been discretized into small bins, with the fission sources integrated in each bin. This method is not necessarily desirable as the arbitrariness and approximations introduced by discretization can affect the results. In response, this study introduces a new mesh-free method by employing the closest point pair approach in which a fission source generated by perturbation source is moved to the closest fission source and combined there. While involving approximation due to the movement of the fission sources, this mesh-free method circumvents the issues associated with discretization. For perturbations in regions with low fission source density (i.e., near the outer boundary), significant errors arise due to the increased movement distance. To address this issue, we introduce a new method to improve the accuracy of this approach by forcibly increasing the fission sources near the perturbation region. The improved PSM (IPSM) can successfully reproduce results that are comparable to those of the conventional PSM and the reference solution
Kyoto University Academic Day 2025: We are connected to research. Here, we can find what we want to talk about.
No full text京都大学アカデミックデイ2025開催日時: 2025年9月27日（土）11:00-18:00会場: ゼスト御池（京都市役所前地下街：河原町広場、市役所前広場、寺町広場、御幸町広場）、京都市役所本庁舎地下2階オープンスペース主催: 総合研究推進本部（KURA） 共催: 京都市京都大学アカデミックデイ x ホームカミングデイ2025開催日時: 2025年11月1日（土）11:00-17:00会場: 京都大学百周年時計台記念館2階国際交流ホール主催: 総合研究推進本部（KURA） 共催: 成長戦略本部第一部 京都大学アカデミックデイ2025＠ゼスト御池 [4]1. 概要 [4]1-1. 会場配置図 [4]2. プログラム [7]2-1. 研究者と立ち話 [7]2-2. ちゃぶ台囲んで膝詰め対話 [10]2-3. お茶を片手にトーク◎トーク (ゼスト御池開催のみ) [11]2-4. 研究者の本棚 [17]2-5. 附属図書館連携企画 (ゼスト御池開催のみ) [18]3. アンケート [20]3-1. 来場者アンケート [20]3-2. 出展者アンケート [36]3-3. 京都大学アカデミックデイ賞 [49]4. 出展者情報 [52]4-1. 研究者と立ち話 [52]4-2. ちゃぶ台囲んで膝詰め対話 [61]4-3. 出展参加者一覧 [63]第二部 京都大学アカデミックデイ × ホームカミングデイ2025 [67]1. 概要 [67]1-1. 会場配置図 [67]2. プログラム [68]2-1. 研究者と立ち話 [68]2-2. ちゃぶ台囲んで膝詰め対話 [70]2-3. 研究者の本棚 [71]3. アンケート [73]3-1. 来場者アンケート [73]3-2. 出展者アンケート [90]3-3. 京都大学アカデミックデイ賞 [101]4. 出展者情報 [104]4-1. 研究者と立ち話 [104]4-2. ちゃぶ台囲んで膝詰め対話 [110]4-3. 出展参加者一覧 [112]以降の項目は、第一部・第二部まとめて114ページから記載されています。5. その他 [114]5-1. 各種説明会 [114]5-2. 会場間の移動誘導企画 (ゼスト御池のみ) [115]5-3. 「京都大学」をアピールする仕掛け (ゼスト御池のみ) [118]5-4. 広報物 [119]6. 支援体制・準備スケジュール [126]6-1. 支援体制 [126]6-2. スタッフリスト [127]6-3. 準備〜事後スケジュール [128]7. 資料 [129]7-1. ブックリスト [129
The redox driven Na⁺-pumping mechanism in Vibrio cholerae NADH-quinone oxidoreductase relies on dynamic conformational changes
No full text電子のやりとりに連動した構造変化が鍵！コレラ菌の生育に必須のナトリウムポンプのはたらく仕組みを解明. 京都大学プレスリリース. 2026-02-13.What drives a mysterious sodium pump? 京都大学プレスリリース. 2026-02-13.The Na⁺-pumping NADH-quinone oxidoreductase (Na⁺-NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na⁺-pumping across the membrane. Earlier X-ray and cryo-electron microscopy structures of Na⁺-NQR from Vibrio cholerae suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na⁺-NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na⁺ translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides structural insights into the mechanism of Na⁺ translocation coupled to electron transfer in Na⁺-NQR
Classroom analytics with educational big data: A comparative approach for sustainable teacher reflection
No full textThis study investigates the use of educational big data to support classroom analytics, focusing on extracting comparable classroom datasets to enhance teacher reflection. We developed methods to automatically identify and analyze comparable classroom datasets based on student interactions with digital learning materials using log data. Through two analyses, we examined the effectiveness of cosine similarity, the radial basis function (RBF) kernel, and the Jaccard coefficient for identifying comparable classes. Additionally, Dynamic Time Warping (DTW) was used to evaluate classroom engagement patterns. Our results indicate that cosine similarity and the RBF kernel are effective for detecting similarities in classroom data, while the Jaccard coefficient is less dependable. The classroom engagement analysis showed significant differences in engagement patterns across specific classes, offering opportunities for teachers to reflect on and improve their teaching practices. This approach offers a scalable way to gather data and feedback continuously, encouraging ongoing reflections on teaching strategies. Future research should apply these methods in various educational environments to validate their effectiveness
Effects of artificial intelligence assistance on endoscopist performance: Comparison of diagnostic performance in superficial esophageal squamous cell carcinoma detection using video-based models
No full textObjectives: Superficial esophageal squamous cell carcinoma (ESCC) detection is crucial. Although narrow-band imaging improves detection, its effectiveness is diminished by inexperienced endoscopists. The effects of artificial intelligence (AI) assistance on ESCC detection by endoscopists remain unclear. Therefore, this study aimed to develop and validate an AI model for ESCC detection using endoscopic video analysis and evaluate diagnostic improvements. Methods: Endoscopic videos with and without ESCC lesions were collected from May 2020 to January 2022. The AI model trained on annotated videos and 18 endoscopists (eight experts, 10 non-experts) evaluated their diagnostic performance. After 4 weeks, the endoscopists re-evaluated the test data with AI assistance. Sensitivity, specificity, and accuracy were compared between endoscopists with and without AI assistance. Results: Training data comprised 280 cases (140 with and 140 without lesions), and test data, 115 cases (52 with and 63 without lesions). In the test data, the median lesion size was 14.5 mm (range: 1–100 mm), with pathological depths ranging from high-grade intraepithelial to submucosal neoplasia. The model's sensitivity, specificity, and accuracy were 76.0%, 79.4%, and 77.2%, respectively. With AI assistance, endoscopist sensitivity (57.4% vs. 66.5%) and accuracy (68.6% vs. 75.9%) improved significantly, while specificity increased slightly (87.0% vs. 91.6%). Experts demonstrated substantial improvements in sensitivity (59.1% vs. 70.0%) and accuracy (72.1% vs. 79.3%). Non-expert accuracy increased significantly (65.8% vs. 73.3%), with slight improvements in sensitivity (56.1% vs. 63.7%) and specificity (81.9% vs. 89.2%). Conclusions: AI assistance enhances ESCC detection and improves endoscopists' diagnostic performance, regardless of experience
Ahmad Dahlan Revisited: The Ideals and Organizational Structure of Muhammadiyah
No full textMuhammadiyah, a mainstream Islamic organization in Indonesia, was established during the pergerakan (movement) era, when several bumiputra (Indonesian) organizations emerged and demanded their rights. While most of these organizations were relatively short-lived, Muhammadiyah, which was initially unremarkable, developed into a nationwide organization. This paper describes how its founder, K. H. Ahmad Dahlan, laid the organization's foundation and clarified his aims, placing his relationships with other organizations into perspective. Dahlan, a religious official at the Grand Mosque in Yogyakarta, was challenged by the modern school system and began reforming traditional religious education around 1908. Supported by Budi Utomo, Indonesia's first nationalist organization, he built a madrasah, an Islamic school equipped with a modern system. He tried to encourage Muslims to adjust to modern times. Dahlan aimed to bridge the gap between Javanese who enjoyed modern education and the santri who were proficient only in religious knowledge. In the beginning he worked mostly alone, but within a few years he had educated his disciples to become cadres of the organization. He was also involved in Sarekat Islam, the first mass organization advocating for the progress of bumiputra people. Upon learning that Sarekat Islam's leadership had failed to act on their decision to build a school for training Islamic teachers, Dahlan established a special course to train religious preachers who would teach at Muhammadiyah schools and serve as activists for the movement. Meanwhile, concerned about the widespread hostility toward Christianity in Sarekat Islam circles, he advocated for interfaith harmony and emphasized dialogue among religious leaders. Whether it was due to the division between Muslims with little religious knowledge and santri or conflicts between religions, Dahlan feared the fragmentation of society. Through his interactions with other pergerakan groups he built Muhammadiyah's organizational base and revealed his ideals
Drug discovery research with iPSC models of neurodegenerative diseases
No full textInduced pluripotent stem cells (iPSCs) are widely used in research because they can be used to create models of diseases with the same genomic background as in patients. iPSC-based screening is recognized as a valuable approach in drug discovery research. Additionally, efforts are underway to develop high-quality models for drug discovery and to better integrate translational research with clinical studies. This review focuses on neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD), and provides a broad overview of research using iPSCs, ranging from studies of disease mechanisms to applications in drug discovery. Furthermore, several clinical trials based on iPSC research have been initiated, including those of bosutinib, ropinirole, and ezogabine for ALS, and WVE-004 and BII078 for ALS/FTD. Finally, we also wish to highlight screening studies that incorporate artificial intelligence (AI)
A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation
No full textThe secret room a giant virus creates inside its host amoeba. 京都大学プレスリリース. 2026-01-13.巨大ウイルスのmRNA翻訳戦略 --局所環境構築を構築し宿主との競合を回避か？--. 京都大学プレスリリース. 2026-01-09.Many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that deviates from their hosts. However, codon usage patterns that align with the cellular tRNA pool enable efficient translation. How these viruses cope with the mismatch between tRNA supply and demand is unclear. Here we show that Acanthamoeba polyphaga mimivirus (APMV) generates a subcellular area to translate viral mRNAs. tRNA sequencing showed that the tRNA pool was not substantially altered during the infection, even though the virus encodes tRNA genes. Using in situ labelling, we found that viral mRNAs and newly synthesized proteins were localized in the periphery of the viral factory, suggesting that APMV creates a discrete subcellular environment to facilitate translation. Frequently used codons in viral mRNAs had higher tRNA accessibility than the same type of codons in amoeba mRNAs. Our data show how local translation assists the virus in overcoming the mismatch between tRNA supply and demand
Survival in adults with high-risk TA-TMA: a comparative analysis of narsoplimab vs supportive care
No full text移植後TMAにNarsoplimabが有効 --移植後TMAに対する新規治療薬の有効性を国際共同研究で明らかに-- . 京都大学プレスリリース. 2025-10-27.Hematopoietic stem cell transplant–associated thrombotic microangiopathy (TA-TMA) is a potentially fatal multisystem complication of hematopoietic cell transplantation for which there is no approved treatment. In a single-arm study (NCT02222545), narsoplimab treatment for TA-TMA demonstrated a median overall survival (OS) of 274 days from date of diagnosis. Here, we compare OS observed in 2 cohorts treated with narsoplimab to OS in a well-matched external control to test survival benefit in patients with high-risk TA-TMA. OS in patients (aged ≥16 years) with high-risk TA-TMA treated with narsoplimab in a single-arm, open-label study (NCT02222545) or in the narsoplimab expanded access program (EAP; NCT04247906) was compared with OS in a control group with high-risk TA-TMA from the Kyoto Stem Cell Transplantation Group (KSCTG) registry. Narsoplimab-treated patients in the single-arm study (N = 28) had a fourfold reduction in risk of mortality compared with patients from the KSCTG registry (N = 111; hazard ratio [HR], 0.25; 95% confidence interval [CI], 0.19, 0.34; P < .0001). Similarly, in high-risk patients treated with narsoplimab in the EAP (N = 49), mortality risk was significantly lower than among high-risk patients from the KSCTG registry (N = 121; HR 0.38; 95% CI 0.28, 0.51; P < .0001). When narsoplimab-treated patients from the single-arm study and the EAP (N = 77) were compared with KSCTG patients, the HR for mortality was 0.28 (95% CI, 0.22, 0.37; P < .0001). In conclusion, in patients with high-risk TA-TMA, narsoplimab treatment significantly reduced mortality relative to a well-matched external control group who did not receive narsoplimab. These results support narsoplimab as a potential therapeutic option for TA-TMA