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BioImaging Publications

2022
  1. Craig M. Browning, Samantha Mayes, Samuel A. Mayes, Thomas C. Rich, Silas J. Leavesley. Microscopy is better in color: development of a streamlined spectral light path for real-time multiplex fluorescence microscopy. Biomedical Optics Express, (accepted – in press), PMCID: in process

  2. Aritra Bhadraad, April K. Scruggs, Silas J. Leavesley, Naga Annamdevula, April H. George, Andrea L. Britain. Christopher M. Francis, Jennifer M. Knighten, Thomas C. Rich, Natalie N. Bauer. Extracellular vesicle-induced cyclic AMP signaling. Cellular Signaling 95 110348 (2022), PMCID: in process

  3. Thomas C. Rich, Silas J. Leavesley, Angela P. Brandon, Cilina A. Evans, S. Vamsee Raju,  Brant M. Wagener. Phosphodiesterase 4 mediates interleukin-8-induced heterologous desensitization of the β2-adrenergic receptor. FASEB Journal 35: e21946 (2021), PMCID: PMC8483573

  4. Nguyen A, Battle K, Paudel SS, Xu N, Bell J, Ayers L, Chapman C, Singh AP, Palanki S, Rich T, Alvarez DF, Stevens T, Tambe DT. Integrative Toolkit to Analyze Cellular Signals: Forces, Motion, Morphology, and Fluorescence. J Vis Exp. 5:181 (2022), PMCID: in process

  5. Taylor MS, Lowery J, Choi CS, and Francis M. "Restricted Intimal Ca2+ Signaling Associated With Cardiovascular Disease." Frontiers in Physiology 13 848681 (2022)
▼   2021
  1. Ryan Warren, Thomas C. Rich, Silas J. Leavesley, Anh-Vu Phan. A three-dimensional finite element model of cAMP signals. Forces in Mechanics, 4 100041 (2021), PMCID: PMC8773462

  2. Craig M. Browning, Joshua Deal, Sam Mayes, Arslan Arshad, Thomas C. Rich, Silas J. Leavesley. Excitation-scanning hyperspectral video endoscopy: enhancing the light at the end of the tunnel. Biomedical Optics Express, 12:1 247-271 (2021). PMCID: PMC7818959

  3. Xu N, Ayers L, Pastukh V, Alexeyev M, Stevens T, Tambe DT. Impact of Na+ permeation on collective migration of pulmonary arterial endothelial cells. PLoS One. 16:4 e0250095 (2021), PMCID: PMC8064576
▼   2020
  1. Naga S. Annamdevula, Rachel Sweat, Hayden Gunn, John R. Griswold, Andrea L. Britain, Thomas C. Rich, Silas J. Leavesley. Measurement of 3-Dimensional cAMP Distributions in Living Cells using 4-Dimensional (x, y, z, and λ) Hyperspectral FRET Imaging and Analysis. Journal of Visualized Experiments (JoVE), https://www.jove.com/video/61720/. J. Vis. Exp. 164 e61720 (2020). PMCID: PMC7968043 – Under Embargo

  2. Joshua Deal, DJ Pleshinger, Santina C Johnson, Silas J Leavesley, Thomas C Rich. Milestones in the Development and Implementation of FRET-Based Sensors of Intracellular Signals: A Biological Perspective of the History of FRET. Cellular Signaling 75 109769 (2020). PMCID: PMC7679057

  3. Peter F. Favreau, Joshua A. Deal, Bradley Harris, David S. Weber, Thomas C. Rich, Silas J. Leavesley. Label-free spectroscopic tissue characterization using fluorescence excitation-scanning spectral imaging. Journal of Biophotonics, 13:e201900183 (2020). PMCID: PMC8491137  Journal front cover

  4. Mikhail Alexeyev, Aron Geurts, Naga Annamdevula, C. Francis, Silas Leavesley, Thomas Rich, Mark Taylor, Mike Lin, Ron Balczon, Jennifer Knighten, Diego Alvarez, Troy Stevens. Development of an endothelial cell restricted transgenic reporter rat: A resource for physiological studies of vascular biology. American Journal of Physiology – Heart and Circulatory Physiology, 319:2 H349-H358 (2020). PMCID: PMC7473926

  5. Patel NG, Nguyen A, Xu N, Ananthasekar S, Alvarez DF, Stevens T, Tambe DT. Unleashing shear: Role of intercellular traction and cellular moments in collective cell migration. Biochem Biophys Res Commun. 522:2 279-285 (2020), PMCID: PMC6957749

  6. X. Li and N. Gong, “Run-time Deep Learning Enhanced Fast Coding Unit Decision for High Efficiency Video Coding,” Journal of Circuits, Systems, and Computers, 29:3, 2050046-1 - 2050046-19 (2020)

  7. J. Edstrom, H. Das, Y. Xu, and N. Gong, “Memory Optimization for Energy-Efficient Differentially Private Deep Learning,” IEEE Trans. on Very Large Scale Integration (VLSI) Systems, 28:2, 307-316 (2020)

  8. Voth S, Gwin M, Francis M, Frank DW, Pittet JF, Wagener BM, Moser SA, Alexeyev MF, Housley N, Audia JP, Piechocki S, Madera K, Simmons A, Crawford M, Stevens T. “Virulent pseudomonas aeruginosa infection converts antimicrobial amyloids into cytotoxic prions. FASEB J. 2020. The FASEB Journal 34:7, 9156-9179 (2020)

  9. Lee JY, Francis M, Bauer NN, Gassman NR, Stevens T. “A cancer amidst us: The plexiform lesion in pulmonary arterial hypertension.” Am J Physiol Lung Cell Mol Physiol 318:6, L1142-L1144 (2020)
▼   2019
  1. N. Stone, S. Shettlesworth, Thomas C. Rich, Silas J. Leavesley, and Anh-Vu Phan. A Two-Dimensional Finite Element Model of Cyclic Adenosine Monophosphate (CAMP) Intracellular Signaling. SN Applied Sciences 1, no. 12 (2019): 1713. PMCID: PMC7891547

  2. Joshua Deal, Andrea Britain, Thomas Rich, Silas Leavesley. Excitation-Scanning Hyperspectral Imaging Microscopy to Efficiently Discriminate Fluorescence Signals. Journal of Visualized Experiments (JoVE), https://www.jove.com/video/59448/. J. Vis. Exp. 150 e59448 (2019). PMCID: PMC6800214

  3. Patel G, Xu N, Nguyen A, Alvarez DF, Fredberg JJ, Stevens T, Tambe DT. Mechanical signaling in a pulmonary microvascular endothelial cell monolayer. Biochem Biophys Res Commun. 519:2 337-343 (2019), PMCID: PMC6931900

  4. J. Edstrom, D. Chen, Y. Gong, J. Wang, and N. Gong, “Data-Pattern Enabled Self-Recovery Low-Power Storage System for Big Video Data,” IEEE Trans. on Big Data, 5:1, 95-105 (2019)

  5. J. Fu, Z. Liao, N. Gong, and J. Wang, “Mitigating Nonlinear Effect of Memristive Synaptic Device for Neuromorphic Computing,” IEEE Journal on Emerging and Selected Topics in Circuits and Systems, 9:2, 377-387 (2019)

  6. J. Fu, Z. Liao, N. Gong, and J. Wang, “Linear Optimization for Memristive Device in Neuromorphic Hardware,” in Proc. IEEE Computer Society Annual Symposium on VLSI (ISVLSI’19), Miami, FL, (2019) (Best Paper Nomination).
▼   2018
  1. Joshua Deal, Sam Mayes, Craig Browning, Shante Hill, Paul Rider, Carole Boudreaux, Thomas C. Rich, Silas J. Leavesley. Identifying molecular contributors to autofluorescence of neoplastic and normal colon sections using excitation-scanning hyperspectral imaging. Journal of Biomedical Optics 24:2 021207 (2018), PMCID: PMC6307688

  2. Naga S. Annamdevula, Rachael Sweat, John R. Griswold, Kenny Trinh, Chase Hoffman, Savannah West, Joshua Deal, Andrea L. Britain, Kees Jalink, Thomas C. Rich, and Silas J. Leavesley. Spectral imaging of FRET-based sensors reveals sustained cAMP gradients in three spatial dimensions. Cytometry, Part A 93:10 1029-1038 (2018), PMCID: PMC6512796

  3. Ron Balczon, Michael Francis, Silas Leavesley, Troy Stevens, Methods for detecting cytotoxic amyloids following infection of pulmonary endothelial cells by pseudomonas aeruginosa. J. Vis. Exp. 137 e57447 (2018), PMCID: PMC6126449

  4. Silas J. Leavesley, Brenner Sweat, Caitlyn Abbott, Peter Favreau, and Thomas C. Rich. A theoretical-experimental methodology for assessing the sensitivity of biomedical spectral imaging platforms, assays, and analysis methods. Journal of Biophotonics 11:1 1-25 (2018), PMCID: PMC5680159 Journal front cover

  5. Hardin CC, Chattoraj J, Manomohan G, Colombo J, Nguyen T, Tambe D, Fredberg JJ, Birukov K, Butler JP, Del Gado E, Krishnan R. Long-range stress transmission guides endothelial gap formation. Biochem Biophys Res Commun 495:1 749-754 (2018), PMCID: PMC5761675

  6. Mike T. Lin , Ron Balczon , Jean-Francois Pittet , Brant M. Wagener , Stephen A. Moser , K. Adam Morrow , Sarah Voth , C. Michael Francis , Silas Leavesley , Jessica Bell , Diego F. Alvarez , and Troy Stevens. Nosocomial Pneumonia Elicits an Endothelial Proteinopathy: Evidence for a Source of Neurotoxic Amyloids in Critically Ill Patients. American Journal of Respiratory and Critical Care Medicine 198:12 1575-1578 (2018), PMCID: PMC6298632

  7. Shen C, Romero M, Brunelle A, Wolfe C, Blood Q, Dobyns A, Francis M, Taylor MS, Puglisi JL, Longo LD, Wilson CG, Wilson SM. “Long-term high altitude hypoxia influences pulmonary arterial L-type calcium channel-mediated Ca2+ signals and contraction in fetal and adult sheep” Am J Physiol Regul Integr Comp Physiol. 314:3, R433-446 (2018) 
▼   2017
  1. J. Edstrom, Y. Gong, D. Chen, J. Wang, and N. Gong, “Data-Driven Intelligent Efficient Synaptic Storage for Deep Learning,” IEEE Trans. on Circuits and Systems II, 64:12, 1412-1416 (2017)

  2. Tambe DT, Fredberg JJ, Butler JP, Trepat X. Monolayer Stress Microscopy. US Patent 9714932 (2017)
▼   2016
  1. Silas J. Leavesley, Mikayla Walters, Carmen Lopez, Thomas Baker, Peter F. Favreau, Thomas C. Rich, Paul F. Rider, Carole W. Boudreaux. Hyperspectral imaging fluorescence excitation-scanning for colon cancer detection. Journal of Biomedical Optics, 21:10 104003-1 – 104003-11 (2016), PMCID: PMC5084534

  2. Silas J. Leavesley, Thomas C. Rich. Overcoming limitations of FRET measurements. Cytometry, Part A 89:4 325-327 (2016), PMCID: PMC5835960 *Invited, peer-reviewed commentary

  3. Zareian R, Susilo ME, Paten JA, McLean JP, Hollmann J, Karamichos D, Messer CS, Tambe DT, Saeidi N, Zieske JD, Ruberti JW. Human Corneal Fibroblast Pattern Evolution and Matrix Synthesis on Mechanically Biased Substrates. Tissue Eng Part A. 22:19-20 1204-1217 (2016), PMCID: PMC5073220

  4. Francis M, Waldrup J, Qian X, Meriwether J, Solodushko V, Taylor M. “Functional tuning of intrinsic Ca2+ dynamics in swine coronary arteries. Circ Res. 118:7, 1078-1090 (2016)

  5. Francis M, Xu N, Zhou C, Stevens T. “TRPC4 encodes high frequency calcium events in severe pulmonary arterial hypertension”. Am J Path. 186:6,1701-1709 (2016)

  6. Blum-Johnston C, Thorpe RB, Wee C, Romero M, Brunelle AR, Blood Q, Wilson R, Blood AB, Francis M, Taylor MS, Longo LD, Pearce WJ, Wilson SM. “Developmental acceleration of bradykinin-dependent relaxation by prenatal chronic hypoxia impedes normal development after birth”. Am J Physiol Lung Cell Mol Physiol. 310(3): L271-L286 2016
▼   2015
  1. Wenkuan Xin, Wei P. Feinstein, Andrea L. Britain, Cristhiaan D. Ochoa, Bing Zhu, Wito Richter, Silas J. Leavesley, and Thomas C. Rich. Estimating the magnitude of near-membrane PDE4 activity in living cells. American Journal of Physiology – Cell Physiology, 309:6 C415-C424 (2015), PMCID: PMC4572370

  2.  Silas J. Leavesley, Thomas C. Rich. FRET: Signals hidden within the noise. Cytometry, Part A, 85:11 918-920 (2014), PMCID: PMC4360877 *Invited, peer-reviewed commentary

  3. Peter F. Favreau, Clarissa Hernandez, Tiffany Heaster, Diego F. Alvarez, Thomas C. Rich, Prashant Prabhat, & Silas J. Leavesley. An excitation-scanning hyperspectral imaging microscope. Journal of Biomedical Optics, 19:4 046010-1 – 046010-10 (2014), PMCID: PMC3983524

  4. Steward R Jr, Tambe D, Hardin CC, Krishnan R, Fredberg JJ. Fluid shear, intercellular stress, and endothelial cell alignment. Am J Physiol Cell Physiol., 308:8 C657-64 (2015), PMCID: PMC4398851

  5. Tambe DT, Fredberg JJ. And I hope you like jamming too. New J Phys. 17:9 091001 (2015), PMCID: PMC5006935

  6. Park JA, Kim JH, Bi D, Mitchel JA, Qazvini NT, Tantisira K, Park CY, McGill M, Kim SH, Gweon B, Notbohm J, Steward R Jr, Burger S, Randell SH, Kho AT, Tambe DT, Hardin C, Shore SA, Israel E, Weitz DA, Tschumperlin DJ, Henske EP, Weiss ST, Manning ML, Butler JP, Drazen JM, Fredberg JJ. Unjamming and cell shape in the asthmatic airway epithelium. Nat Mater. 14:10 1040-8 (2015), PMCID: PMC4666305

  7. Park CY, Zhou EH, Tambe D, Chen B, Lavoie T, Dowell M, Simeonov A, Maloney DJ, Marinkovic A, Tschumperlin DJ, Burger S, Frykenberg M, Butler JP, Stamer WD, Johnson M, Solway J, Fredberg JJ, Krishnan R. High-throughput screening for modulators of cellular contractile force. Integr Biol (Camb) 7:10 1318-24 (2015), PMCID: PMC4657543

  8. Silas Leavesley. Spectral illumination device and method.  US Patent 10393964 B2 (2015)
▼   2014
  1. Thomas C. Rich, Kristal Webb, Silas J. Leavesley. Perspectives on Cyclic Nucleotide Microdomains and Signaling Specificity: Can we decipher the information content contained within cyclic nucleotide signals? Journal of General Physiology, 143:17-27 (2014), PMCID: PMC3874573

  2. Peter Favreau, Clarissa Hernandez, Ashley Stringfellow Lindsey, Diego F. Alvarez, Thomas C. Rich, Prashant Prabhat, Silas J. Leavesley. Tunable thin-film optical filters for hyperspectral microscopy. Journal of Biomedical Optics, 19:1 011017-1 – 011017-11 (2014), PMCID: PMC3784641
▼   2013
  1. Naga S. Annamdevula, Brenner Sweat, Peter Favreau, Ashley S. Lindsey, Diego F. Alvarez, Thomas C. Rich, Silas J. Leavesley. An approach for characterizing and comparing hyperspectral microscopy systems. Sensors,  13:7 9267-9293 (2013), PMCID: PMC3758648