@article{huang_callahan_wu_holloway_brochu_lu_peng_tzeng_2022, title={Phylogeny-guided microbiome OTU-specific association test (POST)}, volume={10}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01266-3}, abstractNote={AbstractBackgroundThe relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in adata-supervisedfashion.ResultsIn this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods.ConclusionsUsing POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R packagePOSTmwhich is freely available on CRAN (https://CRAN.R-project.org/package=POSTm).}, number={1}, journal={MICROBIOME}, author={Huang, Caizhi and Callahan, Benjamin John and Wu, Michael C. and Holloway, Shannon T. and Brochu, Hayden and Lu, Wenbin and Peng, Xinxia and Tzeng, Jung-Ying}, year={2022}, month={Jun} }
 @article{rasipuram_wu_kuznetsov_kuznetsov_levine_jasper_saveliev_2013, title={Submicrometre particle filtration with a dc activated plasma textile}, volume={47}, ISSN={0022-3727 1361-6463}, url={http://dx.doi.org/10.1088/0022-3727/47/2/025201}, DOI={10.1088/0022-3727/47/2/025201}, abstractNote={Plasma textiles are novel fabrics incorporating the advantages of cold plasma and low-cost non-woven or woven textile fabrics. In plasma textiles, electrodes are integrated into the fabric, and a corona discharge is activated within and on the surface of the fabric by applying high voltages above 10 kV between the electrodes. When the plasma textile is activated, submicrometre particles approaching the textile are charged by the deposition of ions and electrons produced by the corona, and then collected by the textile material. A stable plasma discharge was experimentally verified on the surface of the textile that was locally smooth but not rigid. A filtration efficiency close to 100% was observed in experiments conducted on salt particles with diameters ranging from 50 to 300 nm. Unlike conventional fibrous filters, the plasma textile provided uniform filtration in this range, without exhibiting a maximum particle penetration size.}, number={2}, journal={Journal of Physics D: Applied Physics}, publisher={IOP Publishing}, author={Rasipuram, S C and Wu, M and Kuznetsov, I A and Kuznetsov, A V and Levine, J F and Jasper, W J and Saveliev, A V}, year={2013}, month={Dec}, pages={025201} }
 @article{wu_jasper_kuznetsov_johnson_rasipurarn_2013, title={Submicron particle filtration in monolith filters - A modeling and experimental study}, volume={57}, ISSN={["1879-1964"]}, DOI={10.1016/j.jaerosci.2012.09.002}, abstractNote={With over a million micron-sized channels per square centimeter arranged in a regular pattern on a thin film, monolith filters have significant potential for submicron aerosol particle filtration, even though the filtration process with this class of filters has not been well studied. In order to better understand the capture mechanisms and the main factors that affect the capture efficiency, so as to build predictive numerical models and to improve the design of monolith filters, the filtration process in monolith filters was investigated both experimentally and numerically. Using an electrostatic particle classifier (EPC) and a condensation particle counter (CPC), the experimental platform measured the capture efficiency of salt particles with diameters ranging from 50–300 nm on two monolith filter samples. Based on the filtration process and the repeating geometric structure, a single unit model was proposed. The drag force, electrostatic force, and Brownian motion are considered as the major forces affecting particle motion. Published theories underestimated the capture efficiency compared to the experimental results. The Brownian motion model and the capture criterion were then empirically modified to gain better agreement with the experiment.}, journal={JOURNAL OF AEROSOL SCIENCE}, publisher={Elsevier BV}, author={Wu, Mengbai and Jasper, Warren J. and Kuznetsov, Andrey V. and Johnson, Nathan and Rasipurarn, Srinivasan C.}, year={2013}, month={Mar}, pages={96–113} }
 @article{wu_kuznetsov_jasper_2010, title={Modeling of particle trajectories in an electrostatically charged channel}, volume={22}, ISSN={["1070-6631"]}, DOI={10.1063/1.3369004}, abstractNote={Modeling and analyses of filtration efficiency in electrostatically charged monolith filters are important for evaluating and designing this class of filters. Unlike traditional fibrous filters which comprise external flow around a fiber, monolith filters are modeled as internal flow through small channels. Analogous to single fiber theory for external flows, single channel theory is used to analyze basic fluid mechanics in monolith filters and predict filtration efficiencies. The model incorporates three forces: hydrodynamic forces, electrostatic forces, and Brownian motion. Fluid velocity within the channels is calculated by using an analytical solution for circular channel flow, within which the slip boundary condition is considered because of small length scales. This velocity field is then used to evaluate the drag force on the particle according to Stokes’s law. For this model, a one-way coupling between the fluid flow and the particle motion is assumed due to the fact that the relaxation time for the particles simulated in this paper is very small compared to the time the particles spend in the channel. The electrostatic field is computed assuming a uniform charge distribution on the inner surface of a cylindrical channel of finite length. Using a Monte Carlo simulation, particles are randomly injected into a single channel to determine the filtration efficiency.}, number={4}, journal={PHYSICS OF FLUIDS}, publisher={AIP Publishing}, author={Wu, Mengbai and Kuznetsov, Andrey V. and Jasper, Warren J.}, year={2010}, month={Apr} }