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  1. Article ; Online: Computational healthcare: Present and future perspectives (Review).

    Asai, Ayumu / Konno, Masamitsu / Taniguchi, Masateru / Vecchione, Andrea / Ishii, Hideshi

    Experimental and therapeutic medicine

    2021  Volume 22, Issue 6, Page(s) 1351

    Abstract: Artificial intelligence (AI) has been developed through repeated new discoveries since around 1960. The use of AI is now becoming widespread within society and our daily lives. AI is also being introduced into healthcare, such as medicine and drug ... ...

    Abstract Artificial intelligence (AI) has been developed through repeated new discoveries since around 1960. The use of AI is now becoming widespread within society and our daily lives. AI is also being introduced into healthcare, such as medicine and drug development; however, it is currently biased towards specific domains. The present review traces the history of the development of various AI-based applications in healthcare and compares AI-based healthcare with conventional healthcare to show the future prospects for this type of care. Knowledge of the past and present development of AI-based applications would be useful for the future utilization of novel AI approaches in healthcare.
    Language English
    Publishing date 2021-09-23
    Publishing country Greece
    Document type Journal Article ; Review
    ZDB-ID 2683844-8
    ISSN 1792-1015 ; 1792-0981
    ISSN (online) 1792-1015
    ISSN 1792-0981
    DOI 10.3892/etm.2021.10786
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer.

    Ohno, Ayumu / Umezawa, Kazuo / Asai, Satomi / Kryukov, Kirill / Nakagawa, So / Miyachi, Hayato / Imanishi, Tadashi

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 3436

    Abstract: Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized ... ...

    Abstract Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
    MeSH term(s) Bacteria/genetics ; Coloring Agents/chemistry ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Nanopores ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
    Chemical Substances Coloring Agents ; DNA, Bacterial ; RNA, Bacterial ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2021-02-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-82903-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Scent test using

    Asai, Ayumu / Konno, Masamitsu / Ozaki, Miyuki / Kawamoto, Koichi / Chijimatsu, Ryota / Kondo, Nobuaki / Hirotsu, Takaaki / Ishii, Hideshi

    Oncotarget

    2021  Volume 12, Issue 17, Page(s) 1687–1696

    Abstract: Although early detection and diagnosis are indispensable for improving the prognosis of patients with pancreatic cancer, both have yet to be achieved. Except for pancreatic cancer, other cancers have already been screened through scent tests using ... ...

    Abstract Although early detection and diagnosis are indispensable for improving the prognosis of patients with pancreatic cancer, both have yet to be achieved. Except for pancreatic cancer, other cancers have already been screened through scent tests using animals or microorganisms, including
    Language English
    Publishing date 2021-08-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2560162-3
    ISSN 1949-2553 ; 1949-2553
    ISSN (online) 1949-2553
    ISSN 1949-2553
    DOI 10.18632/oncotarget.28035
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

    Ayumu Ohno / Kazuo Umezawa / Satomi Asai / Kirill Kryukov / So Nakagawa / Hayato Miyachi / Tadashi Imanishi

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 7

    Abstract: Abstract Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we ... ...

    Abstract Abstract Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Direct observation of DNA alterations induced by a DNA disruptor.

    Ohshiro, Takahito / Asai, Ayumu / Konno, Masamitsu / Ohkawa, Mayuka / Komoto, Yuki / Ofusa, Ken / Ishii, Hideshi / Taniguchi, Masateru

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 6945

    Abstract: DNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their relationships. ... ...

    Abstract DNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their relationships. Particularly, DNA alterations caused by exposure to exogenous molecules, such as nucleic acid analogues for cancer therapy and the corresponding changes in cell functions, are of interest in medicine for drug development and diagnosis purposes. However, detection of comprehensive direct evidence for the relationship of DNA modifications/mutations in genes, their effect on transcription factors, and the corresponding cell functions have been limited. In this study, we utilized a single-molecule electrical detection method for the direct observation of DNA alterations on transcription factor binding motifs upon exposure to a nucleic acid analogue, trifluridine (FTD), and evaluated the effects of the DNA alteration on transcriptional activity in cancer cell line cells. We found ~ 10% FTD incorporation at the transcription factor p53 binding regions in cancer cells exposed to FTD for 5 months. Additionally, through single-molecule analysis of p53-enriched DNA, we found that the FTD incorporation at the p53 DNA binding regions led to less binding, likely due to weaken the binding of p53. This work suggests that single-molecule detection of DNA sequence alterations is a useful methodology for understanding DNA sequence alterations.
    MeSH term(s) DNA/chemistry ; Frontotemporal Dementia ; Humans ; Mutation ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism
    Chemical Substances Transcription Factors ; Tumor Suppressor Protein p53 ; DNA (9007-49-2)
    Language English
    Publishing date 2022-04-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-10725-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Hereditary pancreatitis model by blastocyst complementation in mouse.

    Asai, Ayumu / Konno, Masamitsu / Kawamoto, Koichi / Isotani, Ayako / Mori, Masaki / Eguchi, Hidetoshi / Doki, Yuichiro / Arai, Takahiro / Ishii, Hideshi

    Oncotarget

    2020  Volume 11, Issue 22, Page(s) 2061–2073

    Abstract: The application of pluripotent stem cells is expected to contribute to the elucidation of unknown mechanism of human diseases. However, ...

    Abstract The application of pluripotent stem cells is expected to contribute to the elucidation of unknown mechanism of human diseases. However,
    Language English
    Publishing date 2020-06-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2560162-3
    ISSN 1949-2553 ; 1949-2553
    ISSN (online) 1949-2553
    ISSN 1949-2553
    DOI 10.18632/oncotarget.27595
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Direct observation of DNA alterations induced by a DNA disruptor

    Takahito Ohshiro / Ayumu Asai / Masamitsu Konno / Mayuka Ohkawa / Yuki Komoto / Ken Ofusa / Hideshi Ishii / Masateru Taniguchi

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 9

    Abstract: Abstract DNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their ... ...

    Abstract Abstract DNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their relationships. Particularly, DNA alterations caused by exposure to exogenous molecules, such as nucleic acid analogues for cancer therapy and the corresponding changes in cell functions, are of interest in medicine for drug development and diagnosis purposes. However, detection of comprehensive direct evidence for the relationship of DNA modifications/mutations in genes, their effect on transcription factors, and the corresponding cell functions have been limited. In this study, we utilized a single-molecule electrical detection method for the direct observation of DNA alterations on transcription factor binding motifs upon exposure to a nucleic acid analogue, trifluridine (FTD), and evaluated the effects of the DNA alteration on transcriptional activity in cancer cell line cells. We found ~ 10% FTD incorporation at the transcription factor p53 binding regions in cancer cells exposed to FTD for 5 months. Additionally, through single-molecule analysis of p53-enriched DNA, we found that the FTD incorporation at the p53 DNA binding regions led to less binding, likely due to weaken the binding of p53. This work suggests that single-molecule detection of DNA sequence alterations is a useful methodology for understanding DNA sequence alterations.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC.

    Ohshiro, Takahito / Konno, Masamitsu / Asai, Ayumu / Komoto, Yuki / Yamagata, Akira / Doki, Yuichiro / Eguchi, Hidetoshi / Ofusa, Ken / Taniguchi, Masateru / Ishii, Hideshi

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 19304

    Abstract: Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing ...

    Abstract Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.
    MeSH term(s) Adenosine/analogs & derivatives ; Adenosine/isolation & purification ; Adenosine/metabolism ; Cell Line, Tumor ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Cytidine/analogs & derivatives ; Cytidine/isolation & purification ; Cytidine/metabolism ; Epigenesis, Genetic ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Humans ; Methylation ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Sequence Analysis, RNA/methods ; Single Molecule Imaging/methods
    Chemical Substances MIRN200 microRNA, human ; MicroRNAs ; Cytidine (5CSZ8459RP) ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567) ; 5-methylcytidine (TL9PB228DC)
    Language English
    Publishing date 2021-09-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-98805-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC

    Takahito Ohshiro / Masamitsu Konno / Ayumu Asai / Yuki Komoto / Akira Yamagata / Yuichiro Doki / Hidetoshi Eguchi / Ken Ofusa / Masateru Taniguchi / Hideshi Ishii

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of ... ...

    Abstract Abstract Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution.

    Ohshiro, Takahito / Komoto, Yuuki / Konno, Masamitsu / Koseki, Jun / Asai, Ayumu / Ishii, Hideshi / Taniguchi, Masateru

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 3886

    Abstract: Identifying positions at which anticancer drug molecules incorporate into DNA is essential to define mechanisms underlying their activity, but current methodologies cannot yet achieve this. The thymidine fluorine substitution product trifluridine (FTD) ... ...

    Abstract Identifying positions at which anticancer drug molecules incorporate into DNA is essential to define mechanisms underlying their activity, but current methodologies cannot yet achieve this. The thymidine fluorine substitution product trifluridine (FTD) is a DNA-damaging anticancer agent thought to incorporate into thymine positions in DNA. This mechanism, however, has not been directly confirmed. Here, we report a means to detect FTD in a single-stranded oligonucleotide using a method to distinguish single molecules by differences in electrical conductance. Entire sequences of 21-base single-stranded DNAs with and without incorporated drug were determined based on single-molecule conductances of the drug and four deoxynucleosides, the first direct observation of its kind. This methodology may foster rapid development of more effective anticancer drugs.
    MeSH term(s) Algorithms ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; DNA/chemistry ; DNA/metabolism ; Humans ; Quantum Theory ; Sequence Analysis, DNA/instrumentation ; Sequence Analysis, DNA/methods ; Signal Processing, Computer-Assisted ; Trifluridine/chemistry ; Trifluridine/pharmacology ; Water/chemistry
    Chemical Substances Antineoplastic Agents ; Water (059QF0KO0R) ; DNA (9007-49-2) ; Trifluridine (RMW9V5RW38)
    Language English
    Publishing date 2019-03-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-40504-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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