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  1. Article ; Online: Correction: Rigid geometry solves "curse of dimensionality" effects in clustering methods: An application to omics data.

    Adachi, Shun

    PloS one

    2020  Volume 15, Issue 12, Page(s) e0243498

    Abstract: This corrects the article DOI: 10.1371/journal.pone.0179180.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pone.0179180.].
    Language English
    Publishing date 2020-12-03
    Publishing country United States
    Document type Published Erratum
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0243498
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Correction

    Shun Adachi

    PLoS ONE, Vol 15, Iss 12, p e

    Rigid geometry solves "curse of dimensionality" effects in clustering methods: An application to omics data.

    2020  Volume 0243498

    Abstract: This corrects the article DOI:10.1371/journal.pone.0179180.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pone.0179180.].
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Rigid geometry solves "curse of dimensionality" effects in clustering methods: An application to omics data.

    Adachi, Shun

    PloS one

    2017  Volume 12, Issue 6, Page(s) e0179180

    Abstract: The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained ... ...

    Abstract The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained liquid chromatography-mass spectrometry (LC/MS) data of calculated protein signal intensities in HEK-293 cells. Our first attempt at directly clustering the values failed, most likely due to the so-called "curse of dimensionality". The clusters were not reproducible, and the outputs differed with different methods. By utilizing rigid geometry with a prime ideal I-adic (p-adic) metric, however, we rearranged the sample clusters into a meaningful and reproducible order, and the results were the same with each of the different clustering methods tested. Furthermore, we have also succeeded in application of this method to expression array data in similar situations. Thus, we eliminated the "curse of dimensionality" from the data set, at least in clustering methods. It is possible that our approach determines a characteristic value of systems that follow a Boltzmann distribution.
    MeSH term(s) Algorithms ; Chromatography, Liquid/methods ; Cluster Analysis ; HEK293 Cells ; Humans ; Mass Spectrometry/methods ; Proteomics/methods
    Language English
    Publishing date 2017-06-14
    Publishing country United States
    Document type Journal Article
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0179180
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rigid geometry solves "curse of dimensionality" effects in clustering methods

    Shun Adachi

    PLoS ONE, Vol 12, Iss 6, p e

    An application to omics data.

    2017  Volume 0179180

    Abstract: The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained ... ...

    Abstract The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained liquid chromatography-mass spectrometry (LC/MS) data of calculated protein signal intensities in HEK-293 cells. Our first attempt at directly clustering the values failed, most likely due to the so-called "curse of dimensionality". The clusters were not reproducible, and the outputs differed with different methods. By utilizing rigid geometry with a prime ideal I-adic (p-adic) metric, however, we rearranged the sample clusters into a meaningful and reproducible order, and the results were the same with each of the different clustering methods tested. Furthermore, we have also succeeded in application of this method to expression array data in similar situations. Thus, we eliminated the "curse of dimensionality" from the data set, at least in clustering methods. It is possible that our approach determines a characteristic value of systems that follow a Boltzmann distribution.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006 ; 310
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  5. Article: Corrigendum: Dynamic nature of SecA and Its associated proteins in

    Adachi, Shun / Murakawa, Yasuhiro / Hiraga, Sota

    Frontiers in microbiology

    2021  Volume 11, Page(s) 634250

    Abstract: This corrects the article DOI: 10.3389/fmicb.2015.00075.]. ...

    Abstract [This corrects the article DOI: 10.3389/fmicb.2015.00075.].
    Language English
    Publishing date 2021-01-13
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.634250
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Corrigendum: Dynamic nature of SecA and Its associated proteins in

    Adachi, Shun / Murakawa, Yasuhiro / Hiraga, Sota

    Frontiers in microbiology

    2020  Volume 11, Page(s) 595994

    Abstract: This corrects the article DOI: 10.3389/fmicb.2015.00075.]. ...

    Abstract [This corrects the article DOI: 10.3389/fmicb.2015.00075.].
    Language English
    Publishing date 2020-11-25
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.595994
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Corrigenda: SecA defects are accompanied by dysregulation of MukB, DNA gyrase, chromosome partitioning and DNA superhelicity in

    Adachi, Shun / Murakawa, Yasuhiro / Hiraga, Sota

    Microbiology (Reading, England)

    2020  Volume 166, Issue 12, Page(s) 1194

    Language English
    Publishing date 2020-12-23
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.000974
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.140: Show issues Location:
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    Order via subito

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  8. Article ; Online: Commentary: Origin and evolution of pathogenic coronaviruses.

    Adachi, Shun / Koma, Takaaki / Doi, Naoya / Nomaguchi, Masako / Adachi, Akio

    Frontiers in immunology

    2020  Volume 11, Page(s) 811

    MeSH term(s) Coronavirus Infections ; Humans ; Middle East Respiratory Syndrome Coronavirus
    Keywords covid19
    Language English
    Publishing date 2020-04-21
    Publishing country Switzerland
    Document type Journal Article ; Comment
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2020.00811
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Commentary

    Shun Adachi / Takaaki Koma / Naoya Doi / Masako Nomaguchi / Akio Adachi

    Frontiers in Immunology, Vol

    Origin and evolution of pathogenic coronaviruses

    2020  Volume 11

    Keywords COVID-19 ; pathogenic coronaviruses ; SARS-CoV ; MERS-CoV ; SARS-CoV-2 ; origin ; Immunologic diseases. Allergy ; RC581-607 ; covid19
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Biological hierarchies emerged from natural characteristics of a number theory

    Adachi, Shun

    2016  

    Abstract: We would like to show how biological grouping, especially in the case of species formation, is emerged through a nature of interactive populations with a number theory. First, we are able to define a species as a $p$-Sylow subgroup of a particular ... ...

    Abstract We would like to show how biological grouping, especially in the case of species formation, is emerged through a nature of interactive populations with a number theory. First, we are able to define a species as a $p$-Sylow subgroup of a particular community in a single niche, confirmed by topological analysis. We named this model the patch with zeta dominance (PzDom) model. Next, the topological nature of the system is carefully examined. We confirm the induction of hierarchy and time through a one-dimensional probability space with certain topologies. For further clarification of induced fractals including the relation to renormalization, a theoretical development is proposed based on a newly identified fact, namely that scaling parameters for magnetization analogs exactly correspond to imaginary parts of the Riemann zeta function's nontrivial zeros. In our PzDom model, calculations only require knowledge of the density of individuals over time.
    Keywords Quantitative Biology - Populations and Evolution
    Subject code 612
    Publishing date 2016-03-02
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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