Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks.

In this paper, we aim to build a platform that will help bridge the gap between high-dimensional computation and wet-lab experimentation by allowing users to interrogate genomic signatures at multiple molecular levels and identify best next actionable steps for downstream decision making. We introduce Multioviz: a publicly accessible R package and web application platform to easily perform in silico hypothesis testing of generated gene regulatory networks. We demonstrate the utility of Multioviz by conducting an end-to-end analysis in a statistical genetics application focused on measuring the effect of in silico perturbations of complex trait architecture. By using a real dataset from the Wellcome Trust Centre for Human Genetics, we both recapitulate previous findings and propose hypotheses about the genes involved in the percentage of immune CD8+ cells found in heterogeneous stocks of mice. Source code for the Multioviz R package is available at https://github.com/lcrawlab/multio-viz and an interactive version of the platform is available at https://multioviz.ccv.brown.edu/ .

Bottom-Up Synthesized All-Thermal-Catalyst Aerogels for Heat-Regenerative Air Filtration.

Airborne particular matter (PM) pollution is an increasing global issue and alternative sources of filter fibers are now an area of significant focus. Compared with relatively mature hazardous gas treatments, state of the art high-efficiency PM filters still lack thermal decomposition ability for organic PM pollutants, such as soot from coal-fired power plants and waste-combustion incinerators, resulting in frequent replacement, high cost, and second-hand pollution. In this manuscript, we propose a bottom-up synthesis method to make the first all-thermal-catalyst air filter (ATCAF). Self-assembled from ∼50 nm diameter TiO2 fibers, ATCAF could not only capture the combustion-generated PM pollutants with >99.999% efficiency but also catalyze the complete decomposition of the as-captured hydrocarbon pollutants at high temperature. It has the potential of in situ eliminating the PM pollutants from burning of hydrocarbon materials leveraging the burning heat.

Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry.

The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method.

Development of an Abbott ARCHITECT cyclosporine immunoassay without metabolite cross-reactivity.

OBJECTIVE: We investigated the mechanism by which the ARCHITECT cyclosporine (CsA) chemiluminescent microparticle immunoassay (CMIA) eliminates cross-reactivity to CsA metabolites AM1 and AM9, despite its use of a monoclonal antibody which shows cross-reactivity in fluorescence polarization immunoassays. DESIGN AND METHODS: The CMIA was accomplished by incubating an extracted blood sample with magnetic microparticles coated with a very low amount of anti-CsA antibody. After a wash step the microparticles were incubated with a chemiluminescent CsA tracer, followed by a second wash step and measurement of chemiluminescence. The reagent concentrations of salt and detergent were optimized to maximize CsA binding and minimize metabolite interference. RESULTS: Elimination of CsA metabolite cross-reactivity was shown using purified metabolites and blood samples containing native CsA metabolites. The CMIA demonstrated precision and sensitivity acceptable for use in a clinical setting. CONCLUSION: We conclude that it is possible to eliminate CsA metabolite immuno-cross-reactivity by careful assay design.