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.

25) M. Heidelman, B. Dhakal, M. Gikunda, K.P.T. Silva, L. Risal, A.I. Rodriguez, F. Abe, P. Urayama. 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 Feature Paper

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

23) P. Urayama, T. Phillips, T.A. Finn, B. Dhakal, 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). doi:10.1117/12.2578724

22) M. Kreider, A.I. Rodriguez, K. Vishwanath, P. Urayama. “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). doi: 10.1117/12.2546398

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

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

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

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

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

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

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

As Assistant Professor:

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

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

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

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

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

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

Prior to Miami University

8) M.-A. Mycek, P. Urayama, 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 (8 October 2003). doi:10.1117/12.499867

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

6) M.-A. Mycek, P. Urayama, 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 (19 June 2003). doi:10.1117/12.478120

5) P. Urayama, 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: 483-496 (2003). doi:10.1007/s00340-003-1152-4

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

3) D.A. Hajduk, P. Urayama, 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: 7148-7156 (1995). doi:10.1021/ma00125a017

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

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

Master’s Thesis

18) Bibek Dhakal, M.S., 2021. “Developing measures for assessing the detection of chemically induced autofluorescence response under high hydrostatic pressure.”

17) Martin R. Heidelman, M.S., 2019. “Cellular metabolic monitoring at high hydrostatic pressure using phasor analysis of UV-excited autofluorescence.”

16) Nazar Al-Aayedi, M.S., 2018. “Concentration-dependent cyanide action monitored using spectral phasor analysis of UV-excited cellular autofluorescence.”

15) Laxmi Risal, M.S., 2016. “Study of pressure dependence of molecular conformation of NADH using spectral phasor analysis.”

14) Millicent N. Gikunda, M.S., 2016. “An improved sample loading technique for cellular metabolic response monitoring under pressure.”

13) Madhu S. Gaire, M.S., 2016. “Exploring the autofluorescence response to cyanide using spectral phasor analysis.”

12) Maha M. Aljohani, M.S., 2016. “Spectral phasor analysis on absorbance spectra for quantifying the content of dye mixtures.”

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.”

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

9) Zachariah P. Callahan, M.S., 2013. “Utilization of a dual-wavelength dye for the characterization of pH buffers under hydrostatic pressure.”

8) Alison Huff, M.S., 2012. “A hydrostatic pressure perfusion system for biological systems.”

7) Jun Cheng, M.S., 2011. “Monitoring metabolic responses in Saccharomyces cerevisiae using fluorescence-based detection of NADH conformation.”

6) Erik J. Alquist, M.S., 2010. “The effects of high hydrostatic pressure on NADH conformation.”

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.”

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

3) Thomas Haver, M.S., 2007. “The assessment and application of point spread function deconvolution to high pressure fluorescence microscopy imaging.”

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

1) Jacob J. Ajimo, M.S. 2005. “A UV-Visible-NIR, Time-Resolved Fluorescence Spectrometer for High-Pressure Biological Studies.”

Honors Thesis

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

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.

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.

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.

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

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⁺ binding constants.” University Honors with Distinction; Honors, Department of Physics.

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.

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

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.