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Bayesian Classification of Genomic Big Data
Published in Ervin Sejdić, Tiago H. Falk, Signal Processing and Machine Learning for Biomedical Big Data, 2018
Ulisses M. Braga-Neto, Emre Arslan, Upamanyu Banerjee, Arghavan Bahadorinejad
The output of the first round of MS (MS1) provides information about detected peptides, their abundances, and related characteristics. The process of filtering these data and compiling the parent protein abundances from the raw peptide data is called protein abundance roll-up. To obtain the identities of the parent proteins from captured peptide sequence information, one will often use a second round of MS and search available MS/MS (MS2) databases. Alternatively, the accurate mass and time (AMT) approach matches peptides to databases using the monoisotopic mass and elution time predictors, obviating the need of a second step of MS [51]. We assume here that data is available in the form of rolled-up abundances, whereby the readout of protein l in sample j can be written as
Emerging Biomedical Analysis
Published in Lawrence S. Chan, William C. Tang, Engineering-Medicine, 2019
Tandem mass spectrometry (MS/MS or MS2) refers to the combination of two or more mass analyzers in a single mass spectrometer. In a tandem mass spectrometer, ions in a wide mass range are first measured in the first stage of mass spectrometry (MS1); based on the MS1 data, ions within a narrow mass range (precursor ions) are isolated and dissociated; the fragment or product ions are then identified in the second stage of mass spectrometry (MS2). This concept can be extended to multi-stage mass spectrometry (MSn) if the product ions are further isolated, fragmented and measured in the nth stage of mass spectrometry (MSn).
Wastewater Treatment for Water Recycling
Published in Valentina Lazarova, Akiça Bahri, Water Reuse for Irrigation, 2004
MS2 bacteriophage is being increasingly used as an indicator for UV system performance and plant design. MS2 are F-specific bacteriophages (or male-specific), i.e., they adsorb on the F pilus of their bacterial host (coliforms) as the first stage of infection. They are RNA phages; their genetic material consists of a single strand of RNA. This bacteriophage is considered one of the best microorganisms to serve as an indicator of viral inactivation, because it
Demonstrated SARS-CoV-2 Surface Disinfection Using Ozone
Published in Ozone: Science & Engineering, 2021
Savannah J. Volkoff, Trevor J. Carlson, Kelsey Leik, Jacques J. Smith, Duane Graves, Philip Dennis, Taylor Aris, Doug Cuthbertson, Andrew Holmes, Kirk Craig, Bruce Marvin, Eric Nesbit
This is the first successful demonstration of O3 for the disinfection of SARS-CoV-2. Two viral models were evaluated in this work. The first model, Accuplex™, is a recombinant mammalian cell containing enveloped SARS-CoV-2 RNA. This model serves to mimic the structure of SARS-CoV-2. The second model is bacteriophage MS2, which is a non-enveloped virus demonstrated to resist destruction by O3, therefore serving as a conservative model for optimizing O3 concentrations and contact times required for viral disinfection (Alimohammadi and Naderi 2020). Finally, we tested SARS-CoV-2 in effluent from a wastewater treatment plant, which is a matrix currently used to monitor infections in communities (Kitajima et al. 2020; Mcmahan et al. 2020).