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925 results on '"Yamashita, Fumiyoshi"'

3. Complex network prediction using deep learning

Author

Tanaka, Yoshihisa, Kojima, Ryosuke, Ishida, Shoichi, Yamashita, Fumiyoshi, and Okuno, Yasushi

Subjects
Physics - Physics and Society, Computer Science - Social and Information Networks, Quantitative Biology - Molecular Networks
Abstract

Systematic relations between multiple objects that occur in various fields can be represented as networks. Real-world networks typically exhibit complex topologies whose structural properties are key factors in characterizing and further exploring the networks themselves. Uncertainty, modelling procedures and measurement difficulties raise often insurmountable challenges in fully characterizing most of the known real-world networks; hence, the necessity to predict their unknown elements from the limited data currently available in order to estimate possible future relations and/or to unveil unmeasurable relations. In this work, we propose a deep learning approach to this problem based on Graph Convolutional Networks for predicting networks while preserving their original structural properties. The study reveals that this method can preserve scale-free and small-world properties of complex networks when predicting their unknown parts, a feature lacked by the up-to-date conventional methods. An external validation realized by testing the approach on biological networks confirms the results, initially obtained on artificial data. Moreover, this process provides new insights into the retainability of network structure properties in network prediction. We anticipate that our work could inspire similar approaches in other research fields as well, where unknown mechanisms behind complex systems need to be revealed by combining machine-based and experiment-based methods., Comment: 20 pages, 16 figures

Published
2021

4. Dynamic change of gene-to-gene regulatory networks in response to SARS-CoV-2 infection

Author

Tanaka, Yoshihisa, Higashihara, Kako, Nakazawa, Mai Adachi, Yamashita, Fumiyoshi, Tamada, Yoshinori, and Okuno, Yasushi

Subjects
Quantitative Biology - Molecular Networks
Abstract

The current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by researchers globally with the aim of resolving this disruptive crisis. This investigation process is indispensable for an understanding of how SARS-CoV-2 behaves in human host cells. However, little is known about the systematic molecular mechanisms involved in the effect of SARS-CoV-2 infection on human host cells. Here, we have presented gene-to-gene regulatory networks in response to SARS-CoV-2 using a Bayesian network. We examined the dynamic changes of the SARS-CoV-2-purturbated networks established by our proposed framework for gene network analysis, revealing that interferon signaling gradually switches to the subsequent inflammatory-cytokine signaling cascades. Furthermore, we have succeeded in capturing a COVID-19 patient-specific network in which transduction of these signalings is coincidently induced. This enabled us to explore local regulatory systems influenced by SARS-CoV-2 in host cells more precisely at an individual level. Our panel of network analyses has provided new insight into SARS-CoV-2 research from the perspective of cellular systems.

Published
2020

36. Blautia coccoides JCM1395 T Achieved Intratumoral Growth with Minimal Inflammation: Evidence for Live Bacterial Therapeutic Potential by an Optimized Sample Preparation and Colony PCR Method.

Author

Nomura, Shoko, Sukowati, Erike W., Shigeno, Yuko, Takahashi, Maiko, Kato, Akari, Benno, Yoshimi, Yamashita, Fumiyoshi, and Mukai, Hidefumi

Subjects
DNA restriction enzymes, TUMOR necrosis factors, GRAM-positive bacteria, GLASS beads, PEPTIDOGLYCANS
Abstract

We demonstrate that Blautia coccoides JCM1395T has the potential to be used for tumor-targeted live bacterial therapeutics. Prior to studying its in vivo biodistribution, a sample preparation method for reliable quantitative analysis of bacteria in biological tissues was required. Gram-positive bacteria have a thick outer layer of peptidoglycans, which hindered the extraction of 16S rRNA genes for colony PCR. We developed the following method to solve the issue; the method we developed is as follows. The homogenates of the isolated tissue were seeded on agar medium, and bacteria were isolated as colonies. Each colony was heat-treated, crushed with glass beads, and further treated with restriction enzymes to cleave DNAs for colony PCR. With this method, Blautia coccoides JCM1395T and Bacteroides vulgatus JCM5826T were individually detected from tumors in mice intravenously receiving their mixture. Since this method is very simple and reproducible, and does not involve any genetic modification, it can be applied to exploring a wide range of bacterial species. We especially demonstrate that Blautia coccoides JCM1395T efficiently proliferate in tumors when intravenously injected into tumor-bearing mice. Furthermore, these bacteria showed minimal innate immunological responses, i.e., elevated serum tumor necrosis factor α and interleukin-6, similar to Bifidobacterium sp., which was previously studied as a therapeutic agent with a small immunostimulating effect. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Cytosolic Ca2+-dependent Ca2+ release activity primarily determines the ER Ca2+ level in cells expressing the CPVT-linked mutant RYR2

Author

Kurebayashi, Nagomi, primary, Murayama, Takashi, additional, Ota, Ryosaku, additional, Suzuki, Junji, additional, Kanemaru, Kazunori, additional, Kobayashi, Takuya, additional, Ohno, Seiko, additional, Horie, Minoru, additional, Iino, Masamitsu, additional, Yamashita, Fumiyoshi, additional, and Sakurai, Takashi, additional

Published
2022
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