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  1. Article: Catheter Malposition into the Internal Thoracic Vein.

    Fukunaga, Tomohiko

    Chonnam medical journal

    2022  Volume 58, Issue 3, Page(s) 140–141

    Language English
    Publishing date 2022-09-23
    Publishing country Korea (South)
    Document type Case Reports
    ZDB-ID 2536217-3
    ISSN 2233-7393 ; 2233-7385 ; 0377-9564
    ISSN (online) 2233-7393
    ISSN 2233-7385 ; 0377-9564
    DOI 10.4068/cmj.2022.58.3.140
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  2. Article ; Online: Lessons Learned.

    Fukunaga, Tetsuo

    Journal of applied biomechanics

    2021  Volume 37, Issue 3, Page(s) 173–175

    Language English
    Publishing date 2021-04-27
    Publishing country United States
    Document type Editorial
    ZDB-ID 1145288-2
    ISSN 1543-2688 ; 1065-8483
    ISSN (online) 1543-2688
    ISSN 1065-8483
    DOI 10.1123/jab.2021-0066
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  3. Article ; Online: Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets.

    Fukunaga, Tsukasa / Hamada, Michiaki

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2586, Page(s) 163–173

    Abstract: The computational prediction of RNA-RNA interactions has long been studied in RNA informatics. Most of the existing approaches focused on the interaction prediction of short RNAs in small datasets. However, in recent years, two fast prediction methods, ... ...

    Abstract The computational prediction of RNA-RNA interactions has long been studied in RNA informatics. Most of the existing approaches focused on the interaction prediction of short RNAs in small datasets. However, in recent years, two fast prediction methods, RIsearch2 and RIblast, have been developed to predict transcriptome-scale interactions or long RNA interactions. The key idea of the software acceleration of these tools was the integration of a seed-and-extend method, which is used in fast sequence alignment tools, into RNA-RNA interaction prediction. As a result, the two software programs were ten to a thousand times faster than the existing tools; because of this acceleration, detection of genome-wide microRNA target sites or interaction partners of function-unknown long noncoding RNAs has become possible. In this review, we describe the basic concept of the algorithm, its applications, and the future perspectives of the fast RNA-RNA interaction prediction tools.
    MeSH term(s) Transcriptome ; Software ; MicroRNAs/genetics ; Algorithms ; RNA, Long Noncoding/genetics ; Computational Biology/methods
    Chemical Substances MicroRNAs ; RNA, Long Noncoding
    Language English
    Publishing date 2023-01-27
    Publishing country United States
    Document type Review ; Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2768-6_10
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  4. Article: From the standpoint of forensic medicine.

    Fukunaga, Tatsushige

    Chudoku kenkyu : Chudoku Kenkyukai jun kikanshi = The Japanese journal of toxicology

    2019  Volume 30, Issue 1, Page(s) 14–17

    MeSH term(s) Chlorpromazine/adverse effects ; Chlorpromazine/poisoning ; Drug Combinations ; Drug Synergism ; Forensic Medicine/legislation & jurisprudence ; Humans ; Phenobarbital/adverse effects ; Phenobarbital/poisoning
    Chemical Substances Drug Combinations ; vegetamin ; Chlorpromazine (U42B7VYA4P) ; Phenobarbital (YQE403BP4D)
    Language Japanese
    Publishing date 2019-01-22
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 1154823-x
    ISSN 0914-3777
    ISSN 0914-3777
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  5. Article: Preoperative Chronic Inflammation Is a Risk Factor for Postoperative Complications Independent of Body Composition in Gastric Cancer Patients Undergoing Radical Gastrectomy.

    Matsui, Ryota / Inaki, Noriyuki / Tsuji, Toshikatsu / Fukunaga, Tetsu

    Cancers

    2024  Volume 16, Issue 4

    Abstract: The purpose of this study was to investigate the association between preoperative inflammation and postoperative complications in gastric cancer patients having elective gastrectomy. Participants in this study were those who underwent radical gastrectomy ...

    Abstract The purpose of this study was to investigate the association between preoperative inflammation and postoperative complications in gastric cancer patients having elective gastrectomy. Participants in this study were those who underwent radical gastrectomy between April 2008 and June 2018 and were diagnosed with stage I-III primary gastric cancer. Preoperative CRP values were used to divide the patients into two groups: the inflammation group comprised individuals having a CRP level of ≥0.5 mg/dL; the other was the non-inflammation group. The primary outcome was overall complications of Clavien-Dindo grade II or higher after surgery. Using propensity score matching to adjust for background, we compared the postoperative outcomes of the groups and conducted a multivariate analysis to identify risk variables for complications. Of 951 patients, 852 (89.6%) were in the non-inflammation group and 99 (10.4%) were in the inflammation group. After matching, both groups included 99 patients, and no significant differences in patient characteristics were observed between both groups. The inflammation group had a significantly greater total number of postoperative complications (
    Language English
    Publishing date 2024-02-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers16040833
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  6. Article ; Online: Measures to Prevent Disaster-Related Deaths, With a Focus on Earthquake-Prone Japan.

    Inoue, Ken / Takeshita, Haruo / Fujita, Yasuyuki / Fukunaga, Tatsushige

    Asia-Pacific journal of public health

    2024  , Page(s) 10105395241246047

    Language English
    Publishing date 2024-04-10
    Publishing country China
    Document type Letter
    ZDB-ID 1025444-4
    ISSN 1941-2479 ; 1010-5395
    ISSN (online) 1941-2479
    ISSN 1010-5395
    DOI 10.1177/10105395241246047
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  7. Article ; Online: LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.

    Fukunaga, Tsukasa / Hamada, Michiaki

    Bioinformatics advances

    2022  Volume 2, Issue 1, Page(s) vbac078

    Abstract: Motivation: RNA consensus secondary structure prediction from aligned sequences is a powerful approach for improving the secondary structure prediction accuracy. However, because the computational complexities of conventional prediction tools scale with ...

    Abstract Motivation: RNA consensus secondary structure prediction from aligned sequences is a powerful approach for improving the secondary structure prediction accuracy. However, because the computational complexities of conventional prediction tools scale with the cube of the alignment lengths, their application to long RNA sequences, such as viral RNAs or long non-coding RNAs, requires significant computational time.
    Results: In this study, we developed LinAliFold and CentroidLinAliFold, fast RNA consensus secondary structure prediction tools based on minimum free energy and maximum expected accuracy principles, respectively. We achieved software acceleration using beam search methods that were successfully used for fast secondary structure prediction from a single RNA sequence. Benchmark analyses showed that LinAliFold and CentroidLinAliFold were much faster than the existing methods while preserving the prediction accuracy. As an empirical application, we predicted the consensus secondary structure of coronaviruses with approximately 30 000 nt in 5 and 79 min by LinAliFold and CentroidLinAliFold, respectively. We confirmed that the predicted consensus secondary structure of coronaviruses was consistent with the experimental results.
    Availability and implementation: The source codes of LinAliFold and CentroidLinAliFold are freely available at https://github.com/fukunagatsu/LinAliFold-CentroidLinAliFold.
    Supplementary information: Supplementary data are available at
    Language English
    Publishing date 2022-10-22
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbac078
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  8. Article ; Online: Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families.

    Fukunaga, Tsukasa / Iwasaki, Wataru

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 16, Page(s) 4039–4041

    Abstract: Summary: We present Mirage 2.0, which accurately estimates gene-content evolutionary history by considering heterogeneous evolutionary patterns among gene families. Notably, we introduce a deterministic pattern mixture model, which makes Mirage ... ...

    Abstract Summary: We present Mirage 2.0, which accurately estimates gene-content evolutionary history by considering heterogeneous evolutionary patterns among gene families. Notably, we introduce a deterministic pattern mixture model, which makes Mirage substantially faster and more memory-efficient to be applicable to large datasets with thousands of genomes.
    Availability and implementation: The source code is freely available at https://github.com/fukunagatsu/Mirage.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Genome ; Evolution, Molecular ; Biological Evolution ; Dental Porcelain
    Chemical Substances Dental Porcelain (12001-21-7)
    Language English
    Publishing date 2022-06-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac433
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    Zs.A 2374: Show issues Location:
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  9. Article ; Online: Discussion of the features of suicide trends in 1994-1995 and 2019-2020: The need for different contents in suicide prevention measures for both periods in Japan from the viewpoint of the present.

    Inoue, Ken / Fukunaga, Tatsushige

    Legal medicine (Tokyo, Japan)

    2022  Volume 58, Page(s) 102083

    Abstract: Japan is a country that is prone to natural disasters. This study compared the characteristics of suicide trends before and after the Great Hanshin-Awaji Earthquake, and during the current COVID-19 pandemic 25 years later. In the present study, we ... ...

    Abstract Japan is a country that is prone to natural disasters. This study compared the characteristics of suicide trends before and after the Great Hanshin-Awaji Earthquake, and during the current COVID-19 pandemic 25 years later. In the present study, we examined the annual number of suicides, the number of suicides by age group, and the reason for suicide during the period associated with the earthquake (1994-1995) and the period associated with the pandemic (2019-2020). This study used statistical analyses to compare the two periods. Our findings suggest that research needs to be conducted from the perspective of legal medicine and social medicine to devise current and future measures to prevent suicides. During the first period, suicides increased in 1995 compared to 1994. Suicide due to economic and life problems increased significantly. During the second period, suicides increased in 2020 compared to 2019. Suicides by males decreased significantly and those by females increased significantly; suicides by individuals aged 19 or under and by those aged 20-29 increased significantly, while suicides by individuals aged 60-69 decreased significantly; and suicides due to "other problems" increased significantly, while suicides due to economic and life problems decreased significantly. Ongoing studies of detailed trends in suicides due to the effects of COVID-19 need to be conducted in the future, and it is important to determine suicide risk due to the effects of COVID-19. Legal medicine and social medicine are fields that conduct such studies and that can offer science-based responses to these trends.
    MeSH term(s) Adolescent ; Adult ; Aged ; COVID-19/epidemiology ; Disasters ; Earthquakes ; Female ; Humans ; Japan/epidemiology ; Male ; Middle Aged ; Pandemics ; Suicide/prevention & control ; Suicide/trends ; Young Adult
    Language English
    Publishing date 2022-04-30
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 2019555-2
    ISSN 1873-4162 ; 1344-6223
    ISSN (online) 1873-4162
    ISSN 1344-6223
    DOI 10.1016/j.legalmed.2022.102083
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    Zs.A 5250: Show issues Location:
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  10. Article ; Online: Impact of Perioperative Immunonutrition on Postoperative Outcomes in Patients with Upper Gastrointestinal Cancer: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

    Matsui, Ryota / Sagawa, Masano / Inaki, Noriyuki / Fukunaga, Tetsu / Nunobe, Souya

    Nutrients

    2024  Volume 16, Issue 5

    Abstract: There is no consensus on the efficacy of perioperative immunonutrition in patients with upper gastrointestinal (GI) cancer surgery. We clarified the impact of perioperative immunonutrition on postoperative outcomes in patients with upper GI cancers. We ... ...

    Abstract There is no consensus on the efficacy of perioperative immunonutrition in patients with upper gastrointestinal (GI) cancer surgery. We clarified the impact of perioperative immunonutrition on postoperative outcomes in patients with upper GI cancers. We searched MEDLINE (PubMed), MEDLINE (OVID), EMBASE, Cochrane Central Register of Controlled Trials, Web of Science Core Selection, and Emcare from 1981-2022 using search terms related to immunonutrition and upper GI cancer. We included randomized controlled trials. Intervention was defined as immunonutritional therapy, including arginine, n-3 omega fatty acids, or glutamine during the perioperative period. The control was defined as standard nutritional therapy. The primary outcomes were infectious complications, defined as events with a Clavien-Dindo classification grade ≥ II that occurred within 30 days after surgery. After screening, 23 studies were included in the qualitative synthesis and in the quantitative synthesis. The meta-analysis showed that immunonutrition reduced infectious complications (relative risk ratio: 0.72; 95% confidence interval: 0.57-0.92; certainty of evidence: Moderate) compared with standard nutritional therapy. In conclusion, nutritional intervention with perioperative immunonutrition in patients with upper GI cancers significantly reduced infectious complications. The effect of immunonutrition for upper GI cancers in reducing the risk of infectious complications was about 30%.
    MeSH term(s) Humans ; Immunonutrition Diet ; Enteral Nutrition ; Randomized Controlled Trials as Topic ; Gastrointestinal Neoplasms ; Fatty Acids, Omega-3 ; Postoperative Complications/prevention & control
    Chemical Substances Fatty Acids, Omega-3
    Language English
    Publishing date 2024-02-20
    Publishing country Switzerland
    Document type Meta-Analysis ; Systematic Review ; Journal Article ; Review
    ZDB-ID 2518386-2
    ISSN 2072-6643 ; 2072-6643
    ISSN (online) 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu16050577
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