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  1. Article: Three-Dimensional-Printed Instrument for Isothermal Nucleic Acid Amplification with Real-Time Colorimetric Imaging.

    Layne, Tiffany R / Scott, Anchi / Cunha, Larissa L / Turiello, Rachelle / Landers, James P

    Micromachines

    2024  Volume 15, Issue 2

    Abstract: Isothermal amplification methods have become popular in research due to the simplicity of the technology needed to run the reactions. Specifically, loop-mediated isothermal amplification (LAMP) has been widely used for various applications since first ... ...

    Abstract Isothermal amplification methods have become popular in research due to the simplicity of the technology needed to run the reactions. Specifically, loop-mediated isothermal amplification (LAMP) has been widely used for various applications since first reported in 2000. LAMP reactions are commonly monitored with the use of colorimetry. Although color changes associated with positive amplification are apparent to the naked eye, this detection method is subjective due to inherent differences in visual perception from person to person. The objectivity of the colorimetric detection method may be improved by programmed image capture over time with simultaneous heating. As such, the development of a novel, one-step, automated, and integrated analysis system capable of performing these tasks in parallel is detailed herein. The device is adaptable to multiple colorimetric dyes, cost-effective, 3D-printed for single-temperature convective heating, and features an easy-to-use LabVIEW software program developed for automated image analysis. The device was optimized and subsequently validated using four messenger-RNA targets and mock forensic samples. The performance of our device was determined to be comparable to that of a conventional thermal cycler and smartphone image analysis, respectively. Moreover, the outlined system is capable of objective colorimetric analysis, with exceptional throughput of up to 96 samples at once.
    Language English
    Publishing date 2024-02-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2620864-7
    ISSN 2072-666X
    ISSN 2072-666X
    DOI 10.3390/mi15020271
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Increasing threats from SARS-CoV-2 variants: Time to establish global surveillance.

    Layne, Scott P / Taubenberger, Jeffery K

    Science translational medicine

    2021  Volume 13, Issue 601

    MeSH term(s) COVID-19 ; Humans ; Public Health ; RNA, Viral ; SARS-CoV-2
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-06-02
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Intramural
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abj6984
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: More autopsy studies are needed to understand the pathogenesis of severe COVID-19.

    Layne, Scott P / Walters, Kathie-Anne / Kash, John C / Taubenberger, Jeffery K

    Nature medicine

    2022  Volume 28, Issue 3, Page(s) 427–428

    MeSH term(s) Autopsy ; COVID-19 ; Humans ; Lung/pathology ; SARS-CoV-2
    Language English
    Publishing date 2022-02-17
    Publishing country United States
    Document type Letter ; Research Support, N.I.H., Intramural
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-022-01684-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: New coronavirus outbreak: Framing questions for pandemic prevention.

    Layne, Scott P / Hyman, James M / Morens, David M / Taubenberger, Jeffery K

    Science translational medicine

    2020  Volume 12, Issue 534

    Abstract: We need to understand and quantify the dominant variables that govern the SARS-CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread. ...

    Abstract We need to understand and quantify the dominant variables that govern the SARS-CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread.
    MeSH term(s) Betacoronavirus/pathogenicity ; COVID-19 ; China/epidemiology ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Epidemiological Monitoring ; Europe/epidemiology ; Forecasting ; Host-Pathogen Interactions ; Humans ; Information Dissemination ; Models, Theoretical ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Public Health ; Quarantine ; SARS-CoV-2 ; Social Conditions ; United States/epidemiology
    Keywords covid19
    Language English
    Publishing date 2020-12-01
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Intramural
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abb1469
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparative Evaluation and Quantitative Analysis of Loop-Mediated Isothermal Amplification Indicators.

    Scott, Anchi T / Layne, Tiffany R / O'Connell, Killian C / Tanner, Nathan A / Landers, James P

    Analytical chemistry

    2020  Volume 92, Issue 19, Page(s) 13343–13353

    Abstract: Loop-mediated isothermal amplification (LAMP) as a diagnostic tool is rapidly gaining recognition and maturity. Among various advantages over traditional polymerase chain reaction, the ability to visually detect amplification by the incorporation of ... ...

    Abstract Loop-mediated isothermal amplification (LAMP) as a diagnostic tool is rapidly gaining recognition and maturity. Among various advantages over traditional polymerase chain reaction, the ability to visually detect amplification by the incorporation of colorimetric indicators is one of its most unique features. There is an overwhelming variety of LAMP indicators in the literature, yet a comprehensive comparative study is lacking. This study evaluates the use of hydroxynaphthol blue, phenol red, calcein, leuco crystal violet, malachite green, and a fluorescent dye for visual detection. A method for objective quantitative analysis using ImageJ is described that is readily implemented in standard and microfluidic workflows. The work here also includes the largest inter-reader variability study involving 24 participants to evaluate these indicators. We found inaccuracies in visual assessment as bias and/or individual-based perception can exist, solidifying the need for objective analysis. There was not a "universal" indicator, although considerations in sample preparation, storage, and applicability are discussed in length.
    MeSH term(s) Colorimetry ; Fluoresceins/analysis ; Fluoresceins/chemistry ; Fluorescent Dyes/chemistry ; Gentian Violet/chemistry ; Humans ; Indicators and Reagents/chemistry ; Lab-On-A-Chip Devices ; Molecular Diagnostic Techniques ; Naphthalenesulfonates/chemistry ; Nucleic Acid Amplification Techniques ; Phenolsulfonphthalein/chemistry ; Rosaniline Dyes/chemistry
    Chemical Substances Fluoresceins ; Fluorescent Dyes ; Indicators and Reagents ; Naphthalenesulfonates ; Rosaniline Dyes ; malachite green (12058M7ORO) ; trisodium 3-hydroxy-4-((2Z)-2-(2-oxo-4-sulfonatonaphthalen-1-ylidene)hydrazinyl)naphthalene-2,7-disulfonate (63451-35-4) ; Phenolsulfonphthalein (I6G9Y0J1OJ) ; Gentian Violet (J4Z741D6O5) ; fluorexon (V0YM2B16TS)
    Language English
    Publishing date 2020-09-21
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c02666
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Optimization of novel loop-mediated isothermal amplification with colorimetric image analysis for forensic body fluid identification.

    Layne, Tiffany / Jackson, Kimberly / Scott, Anchi / Tanner, Nathan A / Piland, Annie / Haverstick, Doris M / Landers, James P

    Journal of forensic sciences

    2021  Volume 66, Issue 3, Page(s) 1033–1041

    Abstract: Accurate presumptive and confirmatory test use for forensic body fluid identification is essential for gaining contextual information for crime scene investigators. Loop-mediated isothermal amplification (LAMP) is an ideal method for forensic body fluid ... ...

    Abstract Accurate presumptive and confirmatory test use for forensic body fluid identification is essential for gaining contextual information for crime scene investigators. Loop-mediated isothermal amplification (LAMP) is an ideal method for forensic body fluid identification because it is highly specific and generates multi-sized amplicon DNA, and successful amplification results can be read out colorimetrically. Here, we show preliminary data on a LAMP method that rapidly identifies body fluids including venous blood, semen, and saliva, based on colorimetric response and image analysis. The method is designed for easy implementation into forensic casework protocols with minimal disruption to DNA analysis. LAMP naturally increases target specificity due to the use of multiple primers for one target and mRNA targets were used for tissue and human specificity. With colorimetric detection as an inherent part of LAMP, samples that are positive or negative for any of the body fluids are readily identified by image capture and analysis, thus eliminating subjectivity. Results show by using the 3D-printed imaging system specific color ranges can be set for easy determination of body fluids. The resulting color change can be seen in <30 min using a universal temperature and primer concentration for all body fluids. This simple method and imaging system allow for minimal hands-on time with objective image analysis and presents a pathway for creating a new potential method for forensic body fluid identification.
    MeSH term(s) Blood Chemical Analysis ; Colorimetry ; Forensic Medicine/methods ; Humans ; Image Processing, Computer-Assisted ; Male ; Molecular Diagnostic Techniques ; Nucleic Acid Amplification Techniques ; Saliva/chemistry ; Semen/chemistry
    Language English
    Publishing date 2021-02-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 219216-0
    ISSN 1556-4029 ; 0022-1198
    ISSN (online) 1556-4029
    ISSN 0022-1198
    DOI 10.1111/1556-4029.14682
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: New coronavirus outbreak: Framing questions for pandemic prevention

    Layne, Scott P / Hyman, James M / Morens, David M / Taubenberger, Jeffery K

    Sci. transl. med

    Abstract: We need to understand and quantify the dominant variables that govern the SARS-CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread. ...

    Abstract We need to understand and quantify the dominant variables that govern the SARS-CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #7128
    Database COVID19

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  8. Article ; Online: New coronavirus outbreak

    Layne, Scott P. / Hyman, James M. / Morens, David M. / Taubenberger, Jeffery K.

    Science Translational Medicine

    Framing questions for pandemic prevention

    2020  Volume 12, Issue 534, Page(s) eabb1469

    Abstract: We need to understand and quantify the dominant variables that govern the SARS–CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread. ...

    Abstract We need to understand and quantify the dominant variables that govern the SARS–CoV-2 outbreak, rather than relying exclusively on confirmed cases and their geospatial spread.
    Keywords General Medicine ; covid19
    Language English
    Publisher American Association for the Advancement of Science (AAAS)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abb1469
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Human influenza surveillance: the demand to expand.

    Layne, Scott P

    Emerging infectious diseases

    2006  Volume 12, Issue 4, Page(s) 562–568

    Abstract: The World Health Organization Influenza Program is one of the best developed and longest running infectious disease surveillance systems that exists. It maintains a worldwide watch of influenza's evolution to assist delivery of appropriately formulated ... ...

    Abstract The World Health Organization Influenza Program is one of the best developed and longest running infectious disease surveillance systems that exists. It maintains a worldwide watch of influenza's evolution to assist delivery of appropriately formulated vaccines in time to blunt seasonal epidemics and unpredictable pandemics. Despite the program's success, however, much more is possible with today's advanced technologies. This article summarizes ongoing human influenza surveillance activities worldwide. It shows that the technology to establish a high-throughput laboratory network that can process and test influenza viruses more quickly and more accurately is available. It also emphasizes the practical public health and scientific applications of such a network.
    MeSH term(s) Disease Outbreaks/prevention & control ; Evolution, Molecular ; Global Health ; Humans ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza, Human/epidemiology ; Population Surveillance/methods
    Language English
    Publishing date 2006-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1380686-5
    ISSN 1080-6040
    ISSN 1080-6040
    DOI 10.3201/eid1204.051198
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Comparative Evaluation and Quantitative Analysis of Loop-Mediated Isothermal Amplification Indicators

    Scott, Anchi T / Layne, Tiffany R / O’Connell, Killian C / Tanner, Nathan A / Landers, James P

    Analytical chemistry. 2020 Aug. 25, v. 92, no. 19

    2020  

    Abstract: Loop-mediated isothermal amplification (LAMP) as a diagnostic tool is rapidly gaining recognition and maturity. Among various advantages over traditional polymerase chain reaction, the ability to visually detect amplification by the incorporation of ... ...

    Abstract Loop-mediated isothermal amplification (LAMP) as a diagnostic tool is rapidly gaining recognition and maturity. Among various advantages over traditional polymerase chain reaction, the ability to visually detect amplification by the incorporation of colorimetric indicators is one of its most unique features. There is an overwhelming variety of LAMP indicators in the literature, yet a comprehensive comparative study is lacking. This study evaluates the use of hydroxynaphthol blue, phenol red, calcein, leuco crystal violet, malachite green, and a fluorescent dye for visual detection. A method for objective quantitative analysis using ImageJ is described that is readily implemented in standard and microfluidic workflows. The work here also includes the largest inter-reader variability study involving 24 participants to evaluate these indicators. We found inaccuracies in visual assessment as bias and/or individual-based perception can exist, solidifying the need for objective analysis. There was not a “universal” indicator, although considerations in sample preparation, storage, and applicability are discussed in length.
    Keywords analytical chemistry ; colorimetry ; comparative study ; diagnostic techniques ; fluorescent dyes ; gentian violet ; loop-mediated isothermal amplification ; malachite green ; phenolsulfonphthalein ; polymerase chain reaction ; quantitative analysis
    Language English
    Dates of publication 2020-0825
    Size p. 13343-13353.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c02666
    Database NAL-Catalogue (AGRICOLA)

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