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  1. AU="Melnyk, Andrew"
  2. AU="Brassart, Bertrand"
  3. AU="Paukshto, Michael"
  4. AU="Rosenberg, Amy S"
  5. AU=Kraus Courtney L
  6. AU="Herman, Andrew"
  7. AU="Xia, Y M"
  8. AU="Antonio, José"
  9. AU="Curci, C"
  10. AU="Baek, Seon-Hwa"
  11. AU="Wei, Xuecong"
  12. AU="Benarroch, Eduardo E."
  13. AU="Modesto Dutari-Valdés, José"
  14. AU="Bot, Merel"
  15. AU="Mackinnon, Alison C"
  16. AU="van Weeghel, Michel"
  17. AU="Halliday, Michael A. K"
  18. AU="Johnston, Carol S"
  19. AU="Bole-Feysot, Christine"
  20. AU="Beverly Rubik"
  21. AU="Nasiri, Asghar"
  22. AU=Han Huan
  23. AU="Pujades-Rodriguez, Mar"
  24. AU="Bertrand, P"
  25. AU="Hinzen, Wolfram"
  26. AU="Daniel Kupka"
  27. AU="Mayer, Tobias"

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Treffer 1 - 10 von insgesamt 11

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  1. Artikel: Materialism.

    Melnyk, Andrew

    Wiley interdisciplinary reviews. Cognitive science

    2012  Band 3, Heft 3, Seite(n) 281–292

    Abstract: Materialism is nearly universally assumed by cognitive scientists. Intuitively, materialism says that a person's mental states are nothing over and above his or her material states, while dualism denies this. Philosophers have introduced concepts (e.g., ... ...

    Abstract Materialism is nearly universally assumed by cognitive scientists. Intuitively, materialism says that a person's mental states are nothing over and above his or her material states, while dualism denies this. Philosophers have introduced concepts (e.g., realization and supervenience) to assist in formulating the theses of materialism and dualism with more precision, and distinguished among importantly different versions of each view (e.g., eliminative materialism, substance dualism, and emergentism). They have also clarified the logic of arguments that use empirical findings to support materialism. Finally, they have devised various objections to materialism, objections that therefore serve also as arguments for dualism. These objections typically center around two features of mental states that materialism has had trouble in accommodating. The first feature is intentionality, the property of representing, or being about, objects, properties, and states of affairs external to the mental states. The second feature is phenomenal consciousness, the property possessed by many mental states of there being something it is like for the subject of the mental state to be in that mental state. WIREs Cogn Sci 2012, 3:281-292. doi: 10.1002/wcs.1174 For further resources related to this article, please visit the WIREs website.
    Sprache Englisch
    Erscheinungsdatum 2012-05
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2553336-8
    ISSN 1939-5086 ; 1939-5078
    ISSN (online) 1939-5086
    ISSN 1939-5078
    DOI 10.1002/wcs.1174
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Using earth mover's distance for viral outbreak investigations.

    Melnyk, Andrew / Knyazev, Sergey / Vannberg, Fredrik / Bunimovich, Leonid / Skums, Pavel / Zelikovsky, Alex

    BMC genomics

    2020  Band 21, Heft Suppl 5, Seite(n) 582

    Abstract: Background: RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host's immune system and makes them particularly dangerous. Viral outbreaks pose a significant ... ...

    Abstract Background: RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host's immune system and makes them particularly dangerous. Viral outbreaks pose a significant threat for public health, and, in order to deal with it, it is critical to infer transmission clusters, i.e., decide whether two viral samples belong to the same outbreak. Next-generation sequencing (NGS) can significantly help in tackling outbreak-related problems. While NGS data is first obtained as short reads, existing methods rely on assembled sequences. This requires reconstruction of the entire viral population, which is complicated, error-prone and time-consuming.
    Results: The experimental validation using sequencing data from HCV outbreaks shows that the proposed algorithm can successfully identify genetic relatedness between viral populations, infer transmission direction, transmission clusters and outbreak sources, as well as decide whether the source is present in the sequenced outbreak sample and identify it.
    Conclusions: Introduced algorithm allows to cluster genetically related samples, infer transmission directions and predict sources of outbreaks. Validation on experimental data demonstrated that algorithm is able to reconstruct various transmission characteristics. Advantage of the method is the ability to bypass cumbersome read assembly, thus eliminating the chance to introduce new errors, and saving processing time by allowing to use raw NGS reads.
    Mesh-Begriff(e) Algorithms ; Disease Outbreaks ; Hepacivirus/genetics ; High-Throughput Nucleotide Sequencing ; RNA Viruses
    Sprache Englisch
    Erscheinungsdatum 2020-12-16
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-020-06982-4
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering.

    Melnyk, Andrew / Mohebbi, Fatemeh / Knyazev, Sergey / Sahoo, Bikram / Hosseini, Roya / Skums, Pavel / Zelikovsky, Alex / Patterson, Murray

    Journal of computational biology : a journal of computational molecular cell biology

    2021  Band 28, Heft 11, Seite(n) 1113–1129

    Abstract: The availability of millions of SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus-2) sequences in public databases such as GISAID (Global Initiative on Sharing All Influenza Data) and EMBL-EBI (European Molecular Biology Laboratory-European ... ...

    Abstract The availability of millions of SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus-2) sequences in public databases such as GISAID (Global Initiative on Sharing All Influenza Data) and EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute) (the United Kingdom) allows a detailed study of the evolution, genomic diversity, and dynamics of a virus such as never before. Here, we identify novel variants and subtypes of SARS-CoV-2 by clustering sequences in adapting methods originally designed for haplotyping intrahost viral populations. We asses our results using clustering entropy-the first time it has been used in this context. Our clustering approach reaches lower entropies compared with other methods, and we are able to boost this even further through gap filling and Monte Carlo-based entropy minimization. Moreover, our method clearly identifies the well-known Alpha variant in the U.K. and GISAID data sets, and is also able to detect the much less represented (<1% of the sequences) Beta (South Africa), Epsilon (California), and Gamma and Zeta (Brazil) variants in the GISAID data set. Finally, we show that each variant identified has high selective fitness, based on the growth rate of its cluster over time. This demonstrates that our clustering approach is a viable alternative for detecting even rare subtypes in very large data sets.
    Mesh-Begriff(e) Brazil ; Cluster Analysis ; Computational Biology/methods ; Databases, Genetic ; Entropy ; Humans ; Monte Carlo Method ; South Africa ; United Kingdom ; United States
    Sprache Englisch
    Erscheinungsdatum 2021-10-25
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2021.0302
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: From Alpha to Zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering

    Melnyk, Andrew / Mohebbi, Fatemeh / Knyazev, Sergey / Sahoo, Bikram / Hosseini, Roya / Skums, Pavel / Zelikovskiy, Alexandr / Patterson, Murray D

    bioRxiv

    Abstract: The availability of millions of SARS-CoV-2 sequences in public databases such as GISAID and EMBL-EBI (UK) allows a detailed study of the evolution, genomic diversity and dynamics of a virus like never before. Here we identify novel variants and subtypes ... ...

    Abstract The availability of millions of SARS-CoV-2 sequences in public databases such as GISAID and EMBL-EBI (UK) allows a detailed study of the evolution, genomic diversity and dynamics of a virus like never before. Here we identify novel variants and subtypes of SARS-CoV-2 by clustering sequences in adapting methods originally designed for haplotyping intra-host viral populations. We asses our results using clustering entropy --- the first time it has been used in this context. Our clustering approach reaches lower entropies compared to other methods, and we are able to boost this even further through gap filling and Monte Carlo based entropy minimization. Moreover, our method clearly identifies the well-known Alpha variant in the UK and GISAID datasets, but is also able to detect the much less represented (<1% of the sequences) Beta (South Africa), Epsilon (California), Gamma and Zeta (Brazil) variants in the GISAID dataset. Finally, we show that each variant identified has high selective fitness, based on the growth rate of its cluster over time. This demonstrates that our clustering approach is a viable alternative for detecting even rare subtypes in very large datasets.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2021-08-27
    Verlag Cold Spring Harbor Laboratory
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2021.08.26.457874
    Datenquelle COVID19

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  5. Buch: A physicalist manifesto

    Melnyk, Andrew

    thoroughly modern materialism

    (Cambridge studies in philosophy)

    2003  

    Verfasserangabe Andrew Melnyk
    Serientitel Cambridge studies in philosophy
    Schlagwörter Materialism ; Physikalismus ; Reduktionismus ; Materialismus ; Naturphilosophie
    Sprache Englisch
    Umfang XII, 327 S., 23,5 cm
    Verlag Cambridge Univ. Press
    Erscheinungsort Cambridge u.a.
    Dokumenttyp Buch
    Anmerkung Literaturverz. S. 311 - 321
    ISBN 0521827116 ; 9780521827119
    Datenquelle Katalog der Technische Informationsbibliothek Hannover

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  6. Buch ; Online: A physicalist manifesto

    Melnyk, Andrew

    thoroughly modern materialism

    (Cambridge studies in philosophy)

    2003  

    Abstract: A Physicalist Manifesto is the fullest treatment yet of the comprehensive physicalist view that, in some important sense, everything is physical. Andrew Melnyk argues that the view is best formulated by appeal to a carefully worked-out notion of ... ...

    Körperschaft ebrary, Inc
    Verfasserangabe Andrew Melnyk
    Serientitel Cambridge studies in philosophy
    Abstract A Physicalist Manifesto is the fullest treatment yet of the comprehensive physicalist view that, in some important sense, everything is physical. Andrew Melnyk argues that the view is best formulated by appeal to a carefully worked-out notion of realization, rather than supervenience; that, so formulated, physicalism must be importantly reductionist; that it need not repudiate causal and explanatory claims framed in non-physical language; and that it has the a posteriori epistemic status of a broad-scope scientific hypothesis
    Schlagwörter Materialism
    Sprache Englisch
    Umfang Online-Ressource (xii, 327 p), 24 cm
    Verlag Cambridge University Press
    Erscheinungsort Cambridge, U.K ;New York
    Dokumenttyp Buch ; Online
    Anmerkung Includes bibliographical references (p. 311-321) and index
    ISBN 0521827116 ; 9780521827119
    Datenquelle Katalog der Technische Informationsbibliothek Hannover

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  7. Artikel ; Online: Inference of genetic relatedness between viral quasispecies from sequencing data.

    Glebova, Olga / Knyazev, Sergey / Melnyk, Andrew / Artyomenko, Alexander / Khudyakov, Yury / Zelikovsky, Alex / Skums, Pavel

    BMC genomics

    2017  Band 18, Heft Suppl 10, Seite(n) 918

    Abstract: Background: RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such ... ...

    Abstract Background: RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations.
    Results: We present (i) an evolutionary simulation algorithm Viral Outbreak InferenCE (VOICE) inferring genetic relatedness, (ii) an algorithm MinDistB detecting possible transmission using minimal distances between intra-host viral populations and sizes of their relative borders, and (iii) a non-parametric recursive clustering algorithm Relatedness Depth (ReD) analyzing clusters' structure to infer possible transmissions and their directions. All proposed algorithms were validated using real sequencing data from HCV outbreaks.
    Conclusions: All algorithms are applicable to the analysis of outbreaks of highly heterogeneous RNA viruses. Our experimental validation shows that they can successfully identify genetic relatedness between viral populations, as well as infer transmission clusters and outbreak sources.
    Mesh-Begriff(e) Algorithms ; Cluster Analysis ; Computational Biology ; Genome, Viral/genetics ; Hepacivirus/genetics ; Phylogeny ; Quasispecies/genetics ; RNA, Viral/genetics ; Sequence Analysis, RNA
    Chemische Substanzen RNA, Viral
    Sprache Englisch
    Erscheinungsdatum 2017-12-06
    Erscheinungsland England
    Dokumenttyp Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-017-4274-5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.

    Knyazev, Sergey / Tsyvina, Viachaslau / Shankar, Anupama / Melnyk, Andrew / Artyomenko, Alexander / Malygina, Tatiana / Porozov, Yuri B / Campbell, Ellsworth M / Switzer, William M / Skums, Pavel / Mangul, Serghei / Zelikovsky, Alex

    Nucleic acids research

    2021  Band 49, Heft 17, Seite(n) e102

    Abstract: Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to ... ...

    Abstract Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.
    Mesh-Begriff(e) Algorithms ; COVID-19/diagnosis ; COVID-19/virology ; Computational Biology/methods ; Gene Frequency ; HIV Infections/diagnosis ; HIV Infections/virology ; HIV-1/genetics ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; Polymorphism, Single Nucleotide ; RNA Virus Infections/diagnosis ; RNA Virus Infections/virology ; RNA Viruses/genetics ; Reproducibility of Results ; SARS-CoV-2/genetics ; Sensitivity and Specificity
    Sprache Englisch
    Erscheinungsdatum 2021-07-02
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab576
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 1067: Hefte anzeigen Standort:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  9. Buch ; Konferenzbeitrag: IS&T final program and proceedings / IS&T's Tenth International Congress on Advances in Non-Impact Printing Technologies : tenth anniversary congress, 1981-1994, October 30 - November 4, 1994, the Sheraton New Orleans Hotel, New Orleans, Louisiana

    Hays, Dan / Melnyk, Andrew

    1994  

    Körperschaft Society for Imaging Science and Technology
    Veranstaltung/Kongress International Congress on Advances in Non-Impact Printing Technologies (10, 1994.10.30-11.04, NewOrleansLa.)
    Verfasserangabe general chair: Dan Hays, publications chair: Andrew Melnyk
    Umfang XXVII, 608 S
    Erscheinungsort Springfield, Va
    Dokumenttyp Buch ; Konferenzbeitrag
    ISBN 0892081791 ; 9780892081790
    Datenquelle Katalog der Technische Informationsbibliothek Hannover

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  10. Artikel ; Online: Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

    Knyazev, Sergey / Tsyvina, Viachaslau / Shankar, Anupama / Melnyk, Andrew / Artyomenko, Alexander / Malygina, Tatiana / Porozov, Yuri B. / Campbell, Ellsworth M. / Mangul, Serghei / Switzer, William M. / Skums, Pavel / Zelikovsky, Alex

    bioRxiv

    Abstract: Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to ... ...

    Abstract Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing (NGS), but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.
    Schlagwörter covid19
    Verlag BioRxiv
    Dokumenttyp Artikel ; Online
    DOI 10.1101/264242
    Datenquelle COVID19

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