{"id":131,"date":"2022-01-01T14:22:35","date_gmt":"2022-01-01T19:22:35","guid":{"rendered":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/?page_id=131"},"modified":"2023-07-25T15:39:16","modified_gmt":"2023-07-25T19:39:16","slug":"peer-reviewed","status":"publish","type":"page","link":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/peer-reviewed\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

updated July 2023.<\/sup><\/em><\/p>\n\n\n\n

Peer-reviewed journal and conference papers<\/h2>\n\n\n\n

Students are actively involved in all stages of research. Undergraduate<\/span> authors are underlined, and graduate-student authors are italicized<\/em>.<\/p>\n\n\n\n

26) P. Urayama<\/strong>, M. McNeill<\/em>, B. McClain<\/span>, N. Majer<\/span>, and K. Vishwanath. \u201cUV-excited autofluorescence responses from cells embedded in turbid media containing hemoglobin analyzed using spectral phasors,\u201d Proceedings of SPIE 12391, Label-free Biomedical Imaging and Sensing (LBIS) 2023, 123910I (16 March 2023). 7 pages<\/em> doi:10.1117\/12.2650783<\/a><\/p>\n\n\n\n

25) M. Heidelman<\/em>, B. Dhakal<\/em>, M. Gikunda<\/em>, K.P.T. Silva, L. Risal<\/em>, A.I. Rodriguez<\/span>, F. Abe, P. Urayama<\/strong>. Cellular NADH and NADPH conformation as a real time fluorescence-based metabolic indicator under pressurized conditions. Molecules, 26: 5020 (2021). doi.org:10.3390\/molecules26165020<\/a> Feature Paper<\/em><\/p>\n\n\n\n

24) A.H. Short<\/span>, N. Al Aayedi<\/em>, M. Gaire<\/em>, M. Kreider<\/span>, C.K. Wong<\/span>, P. Urayama<\/strong>. Distinguishing chemically induced NADPH- and NADH-related metabolic response using phasor analysis of UV-excited autofluorescence. RSC Advances, 11<\/strong>: 18757-18767 (2021). doi:10.1039\/D1RA02648H<\/a><\/p>\n\n\n\n

23) P. Urayama<\/strong>, T. Phillips<\/span>, T.A. Finn<\/span>, B. Dhakal<\/em>, K. Vishwanath. “Distinguishing cellular respiration vs. oxidative stress in turbid media using UV-excited autofluorescence spectroscopy,” Proceedings of SPIE 11655, Label-free Biomedical Imaging and Sensing (LBIS) 2021, 1165507 (5 March 2021). 8 pages<\/em> doi:10.1117\/12.2578724<\/a><\/p>\n\n\n\n

22) M. Kreider<\/span>, A.I. Rodriguez<\/span>, K. Vishwanath, P. Urayama<\/strong>. “Spectral phasor analysis of autofluorescence responses from cells embedded in turbid media containing collagen,” Proceedings of SPIE 11251, Label-free Biomedical Imaging and Sensing (LBIS) 2020, 112510B (20 February 2020). 10 pages<\/em> doi: 10.1117\/12.2546398<\/a><\/p>\n\n\n\n

21) J. Maltas<\/em>, D. Palo<\/span>, C.K. Wong<\/span>, S. Stefan<\/span>, J. O’Connor<\/span>, N. Al Aayedi<\/em>, M. Gaire<\/em>, D. Kinn<\/span>, P. Urayama<\/strong>. A metabolic interpretation for the response of cellular autofluorescence to chemical perturbations assessed using spectral phasor analysis. RSC Advances, 8<\/strong>: 41526-41535 (2018). doi:10.1039\/C8RA07691J<\/a><\/p>\n\n\n\n

20) D. Palo<\/span>, J. Maltas<\/em>, L. Risal<\/em>, P. Urayama<\/strong>. Sensing NADH conformation using phasor analysis on fluorescence spectra. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 186<\/strong>: 105-111 (2017). doi:10.1016\/j.saa.2017.06.013<\/a><\/p>\n\n\n\n

19) J. Maltas<\/em>, L. Amer<\/span>, Z. Long<\/em>, D. Palo<\/span>, A. Oliva<\/span>, J. Folz<\/span>, P. Urayama<\/strong>. Autofluorescence from NADH conformations associated with different pathways monitored using nanosecond-gated spectroscopy and spectral phasor analysis. Analytical Chemistry, 87<\/strong>: 5117-5124 (2015). doi:10.1021\/ac504386x<\/a><\/p>\n\n\n\n

18) Z. Long<\/em>, J. Maltas<\/em>, M.C. Zatt<\/span>, J. Cheng<\/em>,E.J. Alquist<\/em>, A. Brest<\/span>, P. Urayama<\/strong>. The real-time quantification of autofluorescence spectrum shape for the monitoring of mitochondrial metabolism. Journal of Biophotonics, 8<\/strong>: 247-257 (2015). doi:10.1002\/jbio.201300207<\/a><\/p>\n\n\n\n

17) J. Maltas<\/em>, Z. Long<\/em>, A. Huff<\/em>, R. Maloney<\/em>, J. Ryan<\/span>, P. Urayama<\/strong>. A micro-perfusion system for use during real-time physiological studies under high pressure. Review of Scientific Instruments, 85<\/strong>: 106106 (2014). doi:10.1063\/1.4899121<\/a><\/p>\n\n\n\n

16) J. Ryan<\/span>, P. Urayama<\/strong>. Characterizing the dual-wavelength dye indo-1 for calcium-ion sensing under pressure. Analytical Methods, 4<\/strong>: 80-84 (2012). doi:10.1039\/C1AY05486D<\/a><\/p>\n\n\n\n

15) P. Urayama<\/strong>, E.W. Frey<\/span>, S.R. Savage<\/span>. Fluorescent probe dyes for metabolic-ion sensing under high hydrostatic pressures. Annals of the New York Academy of Sciences, 1189<\/strong>: 104-112 (2010). doi:10.1111\/j.1749-6632.2009.05184.x<\/a><\/p>\n\n\n\n

14) H.M. DePedro<\/em>, P. Urayama<\/strong>. Using LysoSensor Yellow\/Blue DND-160 to sense acidic pH under high hydrostatic pressures, Analytical Biochemistry. 384<\/strong>: 359-361 (2009). doi:10.1016\/j.ab.2008.10.007<\/a><\/p>\n\n\n\n

13) S.B. Keller<\/span>, J.A. Dudley<\/span>, K. Binzel<\/span>, J. Jasensky<\/span>, H.M. DePedro<\/em>, E.W. Frey<\/span>, P. Urayama.<\/strong> A calibration approach for rapid fluorescence lifetime determination for applications using time-gated detection and finite pulse width excitation. Analytical Chemistry, 80<\/strong>: 7876-7881 (2008). doi:10.1021\/ac801252q<\/a><\/p>\n\n\n\n

12) P. Urayama<\/strong>, E.W. Frey<\/span>, M.J. Eldridge. A fluid handling system with finger-tightened connectors for biological studies at kilo-atmosphere pressures. Review of Scientific Instruments, 79<\/strong>: 046103 (2008). doi:10.1063\/1.2907245<\/a><\/p>\n\n\n\n

11) T. Haver<\/em>, E.C. Raber<\/em>, P. Urayama<\/strong>. An application of spatial deconvolution to a capillary-based high-pressure chamber for fluorescence microscopy imaging. Journal of Microscopy, 230<\/strong>: 363-371 (2008). doi:10.1111\/j.1365-2818.2008.01994.x<\/a><\/p>\n\n\n\n

10) M. Salerno<\/span>, J. J. Ajimo,<\/em> J. A. Dudley<\/span>, K. Binzel<\/span>, P. Urayama<\/strong>. <\/em>Characterization of dual-wavelength SNAFL and SNARF dyes for pH sensing under high hydrostatic pressures. Analytical Biochemistry, 362<\/strong>: 258-267 (2007). doi:10.1016\/j.ab.2006.12.042<\/a><\/p>\n\n\n\n

9) E.C. Raber<\/em>, J. A. Dudley<\/span>, M. Salerno<\/span>, P. Urayama<\/strong>. A capillary-based, high-pressure chamber for fluorescence microscopy imaging. Review of Scientific Instruments, 77<\/strong>: 096106 (2006). doi:10.1063\/1.2349303<\/a><\/p>\n\n\n\n

Prior to Miami University<\/em><\/p>\n\n\n\n

8) M.-A. Mycek, P. Urayama<\/strong>, W. Zhong, R.D. Sloboda, K.H. Dragnev, E. Dmitrovsky. “Fluorescence spectroscopy and imaging for noninvasive diagnostics: Applications to early cancer detection in the lung,” Proceedings of SPIE 5141, Diagnostic Optical Spectroscopy in Biomedicine II<\/em> (8 October 2003). doi:10.1117\/12.499867<\/a><\/p>\n\n\n\n

7) W. Zhong, P. Urayama<\/strong>, M.-A. Mycek. <\/em>Imaging fluorescence lifetime modulation of a ruthenium-based dye in living cells: the potential for oxygen sensing. Journal of Physics D: Applied Physics, 36<\/strong>: 1689-1695 (2003). doi:10.1088\/0022-3727\/36\/14\/306<\/a><\/p>\n\n\n\n

6) M.-A. Mycek, P. Urayama<\/strong>, K. Heyman, M. Bussey. “Using POPOP’s viscosity dependent lifetime as a picosecond resolution standard in near-UV fluorescence lifetime imaging microscopy,” Proceedings of SPIE 4962, Manipulation and Analysis of Biomolecules, Cells, and Tissues<\/em> (19 June 2003). doi:10.1117\/12.478120<\/a><\/p>\n\n\n\n

5) P. Urayama<\/strong>, W. Zhong, J.A. Beamish, F.K. Minn, R.D. Sloboda, K.H. Dragnev, E. Dmitrovsky, and M.-A. Mycek. A UV-visible-NIR fluorescence lifetime imaging microscope for laser-based biological sensing with picosecond resolution. Applied Physics B, 76<\/strong>: 483-496 (2003). doi:10.1007\/s00340-003-1152-4<\/a><\/p>\n\n\n\n

4) P. Urayama<\/strong>, S.M. Gruner, and G.N. Phillips Jr. Probing substates in sperm whale myoglobin using high pressure crystallography. Structure, 10<\/strong>: 51-60 (2002). doi:10.1016\/S0969-2126(01)00699-2<\/a><\/p>\n\n\n\n

3) D.A. Hajduk, P. Urayama<\/strong>, S.M. Gruner, S. Erramilli, R. Register, K. Brister, and L. J. Fetters. High pressure effects on the disordered phase of block copolymer melts. Macromolecules, 28<\/strong>: 7148-7156 (1995). doi:10.1021\/ma00125a017<\/a><\/p>\n\n\n\n

2) P. Urayama<\/strong> and G. Benford. Modeling energy flow in turbulent beam-plasma experiments. Physics of Plasmas, 2<\/strong>: 2117-2121 (1995). doi:10.1063\/1.871298<\/a><\/p>\n\n\n\n

1) W.W. Heidbrink, D. Adams, S. Drum, K. Evans, J. Manson, T. Price, P. Urayama<\/strong>, F. J. Wessel. Propagation of a narrow plasma beam in an oblique magnetic field. Physics of Fluids B, 4<\/strong>: 3454-3456 (1992). doi:10.1063\/1.860475<\/a><\/p>\n\n\n\n

Master’s Thesis<\/h2>\n\n\n\n

19) Mary McNeill, M.S., 2023. “A spectral phasor approach for monitoring UV-excited autofluorescence response in cellular suspensions having optical absorption.” OhioLINK<\/a><\/p>\n\n\n\n

18) Bibek Dhakal, M.S., 2021. “Developing measures for assessing the detection of chemically induced autofluorescence response under high hydrostatic pressure.” OhioLINK<\/a><\/p>\n\n\n\n

17) Martin R. Heidelman, M.S., 2019. “Cellular metabolic monitoring at high hydrostatic pressure using phasor analysis of UV-excited autofluorescence.” OhioLINK<\/a><\/p>\n\n\n\n

16) Nazar Al-Aayedi, M.S., 2018. “Concentration-dependent cyanide action monitored using spectral phasor analysis of UV-excited cellular autofluorescence.” OhioLINK<\/a><\/p>\n\n\n\n

15) Laxmi Risal, M.S., 2016. “Study of pressure dependence of molecular conformation of NADH using spectral phasor analysis.” OhioLINK<\/a><\/p>\n\n\n\n

14) Millicent N. Gikunda, M.S., 2016. “An improved sample loading technique for cellular metabolic response monitoring under pressure.” OhioLINK<\/a><\/p>\n\n\n\n

13) Madhu S. Gaire, M.S., 2016. “Exploring the autofluorescence response to cyanide using spectral phasor analysis.” OhioLINK<\/a><\/p>\n\n\n\n

12) Maha M. Aljohani, M.S., 2016. “Spectral phasor analysis on absorbance spectra for quantifying the content of dye mixtures.” OhioLINK<\/a><\/p>\n\n\n\n

11) Jeffrey A. Maltas, M.S., 2014. “The spectral phasor approach as a tool for monitoring the autofluorescence of mitochondrial metabolism and its application to high pressure studies.” OhioLINK<\/a><\/p>\n\n\n\n

10) Zac Long, M.S., 2013. “Towards a system for nanosecond-gated, fluorescence based monitoring of cellular responses to high hydrostatic pressures.” OhioLINK<\/a><\/p>\n\n\n\n

9) Zachariah P. Callahan, M.S., 2013. “Utilization of a dual-wavelength dye for the characterization of pH buffers under hydrostatic pressure.” OhioLINK<\/a><\/p>\n\n\n\n

8) Alison Huff, M.S., 2012. “A hydrostatic pressure perfusion system for biological systems.” OhioLINK<\/a><\/p>\n\n\n\n

7) Jun Cheng, M.S., 2011. “Monitoring metabolic responses in Saccharomyces cerevisiae using fluorescence-based detection of NADH conformation.” OhioLINK<\/a><\/p>\n\n\n\n

6) Erik J. Alquist, M.S., 2010. “The effects of high hydrostatic pressure on NADH conformation.” OhioLINK<\/a><\/p>\n\n\n\n

5) M. Junaid Farooqi, M.S., 2009. “Methods for in situ piezophysiological studies: Optical sectioning via structured illumination and fluorescence-based characterization of NADH conformation.” OhioLINK<\/a><\/p>\n\n\n\n

4) Hector Michael DePedro, M.S., 2008. “Characterization of the low pH sensing dye, LysoSensor Yellow\/Blue DND-160, under high hydrostatic pressures.” OhioLINK<\/a><\/p>\n\n\n\n

3) Thomas Haver, M.S., 2007. “The assessment and application of point spread function deconvolution to high pressure fluorescence microscopy imaging.” OhioLINK<\/a><\/p>\n\n\n\n

2) Erica Raber, M.S., 2006. “Spatial resolution characterization of images taken from a capillary-based high pressure chamber for biological imaging studies.” OhioLINK<\/a><\/p>\n\n\n\n

1) Jacob J. Ajimo, M.S. 2005. “A UV-Visible-NIR, Time-Resolved Fluorescence Spectrometer for High-Pressure Biological Studies.” OhioLINK<\/a><\/p>\n\n\n\n

Honors Thesis<\/h2>\n\n\n\n

9) Max Kreider, B.S. mathematics, B.A. physics, B.A. Spanish, 2020. “Towards optics-based metabolic sensing in tissue.” Honors, Department of Physics.<\/p>\n\n\n\n

8) Andrew I. Rodriguez, B.S. biological physics, B.A. biochemistry, 2020. “Developing non-invasive real-time metabolic monitoring using spectral phasors on autofluorescence.” University Honors with Distinction; Honors, Department of Physics.<\/p>\n\n\n\n

7) Audrey Short, B.S. biochemistry, B.A. physics, 2019. “Spectral phasor analysis on UV-excited autofluorescence provides evidence for concentration dependent cyanide mechanism.” University Honors with Distinction; Honors, Department of Physics.<\/p>\n\n\n\n

6) James O’Connor, B.S. biological physics, B.S. biochemistry, 2016. “Monitoring changes in cellular conformations of NADH in yeast during metabolic transitions induced by alcohols.” Honors, Department of Chemistry and Biochemistry.<\/p>\n\n\n\n

5) Michael Zatt, B.A. microbiology, 2013. “Multiplexed sensing of oxygen uptake rate and real-time NADH conformation in S. cerevisiae<\/em>: a method for detecting metabolic state changes.” Honors, Department of Microbiology.<\/p>\n\n\n\n

4) Erik Rotterman, B.S. engineering physics, B.S. biochemistry, 2011. “Testing and implementation of a titration technique for use in the determination of Ca2+<\/sup> binding constants.” University Honors with Distinction; Honors, Department of Physics.<\/p>\n\n\n\n

3) Lauren Regueyra, B.S. engineering physics, 2010. “High pressure effects on the solvent denaturation of NADH probed via fluorescence spectroscopy.” Honors, Department of Physics.<\/p>\n\n\n\n

2) Eric Frey, B.S. physics, 2008. “Fluorescence-based calcium ion sensing at high hydrostatic pressures.” University Honors with Distinction; Honors, Department of Physics.<\/p>\n\n\n\n

1) Michael Maffett, B.S. engineering physics, 2008. “Computations on the role of electrostatics in understanding the effects of pressure on myoglobin structure.” University Honors with Distinction; Honors, Department of Physics.<\/p>\n","protected":false},"excerpt":{"rendered":"

updated July 2023. Peer-reviewed journal and conference papers Students are actively involved in all stages of research. Undergraduate authors are underlined, and graduate-student authors are italicized. 26) P. Urayama, M. McNeill, B. McClain, N. Majer, and K. Vishwanath. \u201cUV-excited autofluorescence responses from cells embedded in turbid media containing hemoglobin analyzed using spectral phasors,\u201d Proceedings of […]<\/p>\n","protected":false},"author":5859,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"page-templates\/full-width.php","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"class_list":["post-131","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/pages\/131","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/users\/5859"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/comments?post=131"}],"version-history":[{"count":0,"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/pages\/131\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.miamioh.edu\/urayama-cellular-biophysics-lab\/wp-json\/wp\/v2\/media?parent=131"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}