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  1. Article ; Online: Analysis of Mouse Vocal Communication (AMVOC): a deep, unsupervised method for rapid detection, analysis and classification of ultrasonic vocalisations

    Stoumpou, Vasiliki / Vargas, César D. M. / Schade, Peter F. / Boyd, J. Lomax / Giannakopoulos, Theodoros / Jarvis, Erich D.

    Bioacoustics. 2023 Mar. 04, v. 32, no. 2 p.199-229

    2023  

    Abstract: Some aspects of the neural mechanisms underlying mouse ultrasonic vocalisations (USVs) are a useful model for the neurobiology of human speech and speech-related disorders. Much of the research on vocalisations and USVs is limited to offline methods and ... ...

    Abstract Some aspects of the neural mechanisms underlying mouse ultrasonic vocalisations (USVs) are a useful model for the neurobiology of human speech and speech-related disorders. Much of the research on vocalisations and USVs is limited to offline methods and supervised classification of USVs, hindering the discovery of new types of vocalisations and the study of real-time free behaviour. To address these issues, we developed AMVOC (Analysis of Mouse VOcal Communication) as a free, open-source software to detect and analyse USVs. When compared to hand-annotated ground-truth USV data, AMVOC’s detection functionality (both offline and online) has high accuracy and outperforms leading methods in noisy conditions. AMVOC also includes an unsupervised deep learning approach that facilitates discovery and analysis of USV data by training a model and clustering USVs based on latent features extracted by a convolutional autoencoder. The clustering is visualised in a graphical user interface (GUI) which allows users to evaluate clustering performance. These results can be used to explore the vocal repertoire space of individual animals. In this way, AMVOC will facilitate vocal analyses in a broader range of experimental conditions and allow users to develop previously inaccessible experimental designs for the study of mouse vocal behaviour.
    Keywords bioacoustics ; computer software ; mice ; models ; rapid methods ; speech ; ultrasonics ; user interface ; vocalization ; Mouse vocalisation ; ultrasonic vocalisations ; social behaviour ; machine learning ; unsupervised ; real-time
    Language English
    Dates of publication 2023-0304
    Size p. 199-229.
    Publishing place Taylor & Francis
    Document type Article ; Online
    ISSN 2165-0586
    DOI 10.1080/09524622.2022.2099973
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: DRUL for school: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2.

    Frank, Mayu O / Blachere, Nathalie E / Parveen, Salina / Hacisuleyman, Ezgi / Fak, John / Luna, Joseph M / Michailidis, Eleftherios / Wright, Samara / Stark, Pamela / Campbell, Ann / Foo, Ashley / Sakmar, Thomas P / Huffman, Virginia / Bergh, Marissa / Goldfarb, Audrey / Mansisidor, Andres / Patriotis, Agata L / Palmquist, Karl H / Poulton, Nicolas /
    Leicher, Rachel / Vargas, César D M / Duba, Irene / Hurley, Arlene / Colagreco, Joseph / Pagane, Nicole / Orange, Dana E / Mora, Kevin / Rakeman, Jennifer L / Fowler, Randal C / Fernandes, Helen / Lamendola-Essel, Michelle F / Didkovsky, Nicholas / Silvera, Leopolda / Masci, Joseph / Allen, Machelle / Rice, Charles M / Darnell, Robert B

    PloS one

    2021  Volume 16, Issue 6, Page(s) e0252949

    Abstract: To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller ... ...

    Abstract To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/μl in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Nucleic Acid Testing ; Child ; Female ; Humans ; Male ; SARS-CoV-2 ; Saliva/virology ; Schools ; Specimen Handling
    Language English
    Publishing date 2021-06-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0252949
    Database MEDical Literature Analysis and Retrieval System OnLINE

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