Publications

Selected Journal Articles —

Contreras, M., Bachman, W., & Long, D. S. (2022) Discrete protein metric (DPM): A new image similarity metric to calculate accuracy of deep learning-generated cell focal adhesion. Micron, 160:103302.

Polk, T, Schmitt, S., Aldrich, J.L., & Long, D. S. (2022) Human dermal microvascular endothelial cell morphological response to fluid shear stress. Microvascular Research, 143:104377.

Aldrich J.L. & Long D.S., In situ fixation and subsequent collection of cultured endothelial cells in a shear flow. MethodX 6:1164-1173, 2019.

Lim, Y.C., McGlashan, S.R., Cooling, M.T., & Long, D. S. Quantifying flow-induced force transmission and morphological variation in an endothelial cell population. Currently in review.

Elsie C. Jacobson; Jo K. Perry; David S. Long; Ada L. Olins; Donald E. Olins; Bryon E. Wright; Mark H. Vickers; Justin M. O'Sullivan. Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells. BMC Biology 16:142, 2018.

Sumets, P., Cater, J., Long, D., & Clarke, R. Electro-poroelastohydrodynamics of the endothelial glycocalyx layer, Journal of Fluid Mechanics, 838:284-319, 2018.

Jacobson, E., Perry, J.K., Long, D.S., Vickers, M.H., & O'Sullivan, J.M. A potential role for genome structure in the translation of mechanical force during immune cell development Nucleus 7(5), 2016.

Long, D.S., Hou, W, Taylor Rennae, S., & McCowan, L. Serum levels of endothelial glycocalyx constituents in women at 20 weeks gestation who later develop gestational diabetes mellitus compared to matched controls: A pilot study, BMJ Open 6(12)::e011244. doi: 10.1136/bmjopen-2016-011244.

Lee, T.C., Long, D. S. & Clarke, R.J. Stokes flow through a cylindrical tube lined with a porous wall of varying thickness: An application to microvascular hemodynamics Journal of Fluid Mechanics 798, 812-852

Lim, Y.C., McGlashan, S.R., Cooling, M.T., & Long, D. S. Culturing and detection of primary cilia in endothelial cell models , Cilia 4:11 (30 September 2015)

Koschwanez, H., Vurnek, M., Weinman, J., Tarlton, J., Whiting, C., Amirapu, S., Colgan, S., Long, D., Jarret, P., & Broadbent, E. Stress-related changes to immune cells in the skin prior to wounding may impair subsequent healing , Brain, Behavior, and Immunity, DOI:10.1016/j.bbi.2015.06.011

Sumets, P., Cater, J., Long, D., & Clarke, R. A boundary-integral representation for biphasic mixture theory with application to the post-capillary glycocalyx , Proceedings of the Royal Society London A, 471:2179.

Lim, Y.C., Cooling, M.T., & Long, D.S. Computational Models of the Primary Cilium and Endothelial Mechanotransmission , Biomechanics and Modeling in Mechanobiology. 14(3), 665-678, (DOI: 10.1007/s10237-014-0629-x)

Long, D.S. & McKay, T.G. A Design Project Based Approach to Teaching Undergraduate Instrumentation, Teaching, Assessment, and Learning for Engineering. DOI:10.1109/TALE.2014.7062557.

Long, D. S., Zhu, H., & Friedman, M. H. (2013) A Microscope-Based Near-Infrared Stereo Imaging System for Quantifying the Motion of the Murine Epicardial Coronary Arteries In Vivo, Journal of Biomedical Optics 18(9) (September 20, 2013) 096013 doi: 10.1117/1.JBO.18.9.096013

Long, D. S., Smith, M. L., Pries, A. R., Ley, K. & Damiano, E. R. (2004) Micro-viscometry reveals re- duced blood viscosity and altered shear rate and stress distributions in microvessels after hemodilution. Proceedings of the National Academy of Sciences USA 101, 10060–10065.

Damiano, E. R., Long, D. S., & Smith, M. L. (2004) Estimation of viscosity profiles using velocimetry data from parallel flows of linearly viscous fluids: Application to microvascular hemodynamics. J. Fluid Mech 512, 1–19.

Damiano, E. R., Long, D. S., El-Khatib, F. H. & Stace, T. M. (2004) On the motion of a sphere in a Stokes flow parallel to a Brinkman half space. J. Fluid Mech. 500, 75–101.

Smith, M. L., Long, D. S., Damiano, E. R. & Ley, K. (2003) High-resolution near-wall micro-particle image velocimetry reveals the presence of a hemodynamically relevant endothelial surface layer in microvessels in vivo. Biophys. J. 85, 637–645.

Book Chapters —

Lim Y.C., Cooling M.T., McGlashan S.R., Long D.S. (2022) Morphological Variation in an Endothelial Cell Population: A Virtual-Cell Model. In: Joldes G., Doyle B., Wittek A., Nielsen P., Miller K. (eds) Computational Biomechanics for Medicine: Towards Translation and Better Patient Outcomes. Springer, Cham. ISBN 978-3-031-09327-2

Lim Y.C., Cooling M.T., McGlashan S.R., Long D.S. (2016) Mechanical Models of Endothelial Mechanotransmission Based on a Population of Cells. In: Joldes G., Doyle B., Wittek A., Nielsen P., Miller K. (eds) Computational Biomechanics for Medicine. Springer, Cham.

Lim Y.C., Cooling M.T., McGlashan S.R., Long D.S. (2017) Quantifying Cytoskeletal Morphology in Endothelial Cells to Enable Mechanical Analysis. In: Joldes G., Doyle B., Wittek A., Nielsen P., Miller K. (eds) Computational Biomechanics for Medicine. Springer, Cham. (to appear)

Conference Abstract-Papers

D. Long (2024) “Prediction and Application Specific Validation of Subcellular Morphology of Endothelial Cells using Machine Learning”. 2nd International Conference on Emerging Materials and Technologies (ICEMT-2024). Pittsburgh, Kansas, USA. 28-29 Mar 2024.

A.A. Bahadori, S-K. Fan, K-L Ho, J. Ding, K. Ginavan, C. Azuma, P. Bhanja, S. Saha, & D. Long (2023) “Radiation Carcinogenesis Biomarker Analysis with a Hydrogel-based Organ-on-a-Chip Sys- tem”. NASA Human Research Program (HRP) Investigators Workshop, To the Moon: The Next Golden Age of Human Spaceflight. Galveston, Texas, USA. 7-9 Feb 2023.

Hafenstine, R., Contreras, M. Bachman, W., & Long, D. S. (2022) “Predicting Subcellular Morphology of Endothelial Cell Clusters from Only the Cell Membrane Using a Machine Learning Framework: Gen- erating Cellular Digital Twins for Mechanobiology. World Congress of Biomechanics. Taipei, Taiwan.

Miguel Contreras, William Bachman, Rex Hafenstine, & Long, D. S., “Predicting Subcellular Morphology of Endothelial Cell Cluster Using Deep Learning, Cellular and Molecular Bioengineering Conference, Indian Wells CA, January 3-7, 2022.

Hafenstine, R. & & Long, D. S., (2022) Using Machine Learning to Predict Subcellular Morphology of Endothelial Cells: Gaining insight into the Mechanisms of Disease through Mechanobiology. BioKansas Innovation Festival. Kansas City KS/MO.

Tabatha Polk, Sarah Schmitt, and & Long, D. S., (2021) “Human Dermal Microvascular Endothelial Cell Response to Laminar Unidirectional Flow, it 7th Micro and Nano Flows Conference, Imperial College London UK, May 24-26 2021. Invited oral presentation.

Yi Chung Lim, Michael Cooling, Sue McGlashan, & & Long, D. S., (2021) “Morphological Variation in an Endothelial Cell Population: A Virtual Cell Model, 24th International Conference on Medical Image Computing & Computer Assisted Intervention, Strasbourg France, September 27 October 1 2021. Invited oral presentation.

Contreras M., Bachman W., Long D.S., Development of an Automatic Computational Machine Learning Pipeline to Process Confocal Fluorescence Images for Virtual Cell Generation. Summer Biomechanics, Bioengineering, & Biotransport Conference. 17-20 June 2020.

Polk T., Schmitt S., Long D.S., Human Dermal Microvascular Endothelial Cells Morphological Response to Fluid Shear Stress. Summer Biomechanics, Bioengineering, & Biotransport Conference. 17-20 June 2020.

Polk T., Schmitt S., Aldrich J., Long D.S., Effects of Fluid Shear Stress on Dermal Human Microvascular Endothelial Cell Morphology. 18th annual Kansas IDeA Network of Biomedical Research Excellence Symposium - Wichita, KS - Honorable Mention

Contreras M. and Long D.S., Development of an Automatic Computational Machine Learning Pipeline to Process Confocal Images for Virtual Cell Generation. 18th annual Kansas IDeA Network of Biomedical Research Excellence Symposium - Wichita, KS

Ali U., Long D.S., Quantification and Analysis of Morphological Changes in Microvascular Endothelial Cells After Exposure to Unidirectional or Pulsatile Flow. 18th annual Kansas IDeA Network of Biomedical Research Excellence Symposium - Wichita, KS

Polk T., Schmitt S., Aldrich J., Long D.S., Impact of Fluid Shear Stress on the Morphology of Dermal Endothelial Cells. Cellular and Molecular Bioengineering Conference - Rio Grande, Puerto Rico

Aldrich, J.A. & Long, D. S. (2019) Dermal Human Microvascular Endothelial Cells Resist Morphological Changes Due to Fluid Shear Stress. Conference for the Society of Engineering Science, St. Louis, MO, USA

Bachman, W. & Long, D. S. (2019) Using Spatial Statistical Modeling and Virtual Cells to Quantify the Morphological Variation in Endothelial Monolayers. Conference for the Society of Engineering Science, St. Louis, MO, USA

Aldrich, J.A. & Long, D. S.c(2019) Effects of Fluid Shear Stress on Chromatin Organization. Cellular and Molecular Bioengineering Conference, San Diego, CA, USA

Bachman, W. & Long, D. S.c(2019) Modeling Framework to Quantify the Force Transmission in Endothelial Cell Clusters: A Cluster-Specific Model and Virtual Multi-Cell Model . Cellular and Molecular Bioengineering Conference, San Diego, CA, USA

Jacobson, E., Perry, J., Vickers, M., Long, D.S., O’Sullivan, J. (2018) Slipping through the cracks: Inac- tive chromatin remodels as a neutrophil migrates through a small pore, American Society of Human Genetics Conference, October 16-20, 2018, San Diego CA USA

Bachman, W. & Long, D. S. (2018) Quantifying Force Transmission and Morphological Variation in Populations of Endothelial Cell Clusters. Undergraduate Research and Creative Activities Forum, Wichita State University

Pherigo, J. & Long, D. S. (2018) Simulation of Morphologically Variant Endothelial Cells in ANSYS.Undergraduate Research and Creative Activities Forum, Wichita State University

Tran, V. & Long, D. S. (2018) Determining Dot Patterns for Micro-Contact Printing. Undergraduate Research and Creative Activities Forum, Wichita State University

Corazza, C., Lim, Y.C.†, & Long, D. S. (2018) Femtosecond Laser Micromachining, Fabrication and Alignment of Circular Microtubes in Hydrogels.2017 Annual Meeting of the Biomedical Engineering Society, Phenoix AZ.

Reece, K. & Long, D. S. (2018) Imaging the Glycocalyx on Human Microvascular Endothelial Cells (HMEC-1). 2018 K-INBRE Symposium, Overland Park, KS, USA (Abstr)

Longhofer, Z. & Long, D. S. (2018) Facilitating an Understanding of a 3-D Virtual Endothelial Cell Population Modeling Framework. 2018 K-INBRE Symposium, Overland Park, KS, USA

Bachman, W. & Long, D. S.∗ (2018) Quantifying Force Transmission and Morphological Variation in Populations of Endothelial Cell Clusters: A Virtual-Cell Approach. 2018 K-INBRE Symposium, Overland Park, KS, USA

Reece, K. & Long, D. S.∗ (2018) Imaging the Glycocalyx on Human Microvascular Endothelial Cells (HMEC-1). Cellular and Molecular Bioengineering Conference, Key Largo, FL, USA

Bachman, W. & Long, D. S. (2018) Force Transmission and Morphological Variation in Populations of Endothelial Cell Clusters. Cellular and Molecular Bioengineering Conference, Key Largo, FL, USA

Kuhl, D. Lim, Y.C., & Long, D. S. (2017) Tensegrity Structures - Computational and Experimental Tensegrity Mechanics. AIP Conference Proceedings, 1863, 410005. https://doi.org/10.1063/1.4992585

Lee, T.C, Clarke, R.J., & Long, D. (2016) Modelling the endothelial glycocalyx layer in the microcirculation24th International Congress of Theoretical and Applied Mechanics, Montreal, Canada, August 21-26, 2016.

Sumetc, P., Cater, J., Long, D., & Clarke, R.J. (2016) Flow through the channel coated with charged porous media 24th International Congress of Theoretical and Applied Mechanics, Montreal, Canada, August 21-26, 2016.

Jacobson, E., Perry, J., Long, D., Vickers, M., & O’Sullivan, J. (2015) Immune cell migration and genome organisation. Liggins Institute Student Research Forum, The University of Auckland, December 1, 2015.

Jacobson E., Perry, J.K., Vickers, M.H., Long, D.S., O’Sullivan, J.M., Slipping through the cracks: Inactive chromatin remodels as a neutrophil migrates through a small pore. American Society of Human Genetics

Lee, T.C, Clarke, R.J., & Long, D. (2016) Modelling the endothelial glycocalyx layer in the microcirculation 24th International Congress of Theoretical and Applied Mechanics, Montreal, Canada, August 21-26, 2016.

Lim, Y.C., Cooling, M.T., McGlashan, S.R., & Long, D. S. (2015) Generation of three-dimensional models suitable for computational mechanical analysis, based on a population of endothelial cells 6th International Conference on Computational Methods, Auckland New Zealand (July 14–17, 2015) (Invited presentation for Yi Chung Lim)

Lim, Y.C., Cooling, M.T., McGlashan, S.R., & Long, D. S. (2014) Modelling Force Transmission of Fluid Shear Stress in Endothelial Cells 7th World Congress of Biomechanics, Boston MA USA (July 6–11, 2014) (Invited presentation for Yi Chung Lim)

Long, D. S., & Lim, Y.C. (2013) A Method to Measure the Site-Specific Aortic Endothelial Cell Gene Expression. 3rd BMES-CMBE Scientific Conference, Waimea, Hawaii, USA (Abstr) (Jan. 2–Jan. 5, 2013).

Lee, T.C., Long, D. S., & Clarke, R.J. (2013) Modelling the effects of a non-uniform endothelial glycocalyx layer in the postcapillary venule. 3rd BMES-CMBE Scientific Conference, Waimea, Hawaii, USA (Abstr) (Jan. 2–Jan. 5, 2013).

Lim, Y.C., Cooling, M.T., & Long, D. S. (2012) Quantifying Endothelial Mechanotransmission. 4th Mechanobiology Symposium, Auckland, New Zealand (Poster) (Dec. 6–Dec. 7, 2012). Note: Y.C. Lim’s presentation voted as best poster presentation.

Lim, Y.C., Cooling, M.T., & Long, D. S. (2012) Endothelial Mechanotransmission. 3rd BMES-CMBE Scientific Conference, Waimea, Hawaii, USA (Abstr) (Jan. 2–Jan. 5, 2012).

Lim, Y.C., Cooling, M., Long, D. S. (2012) Biomechanics of the Primary Cilium. 2012 Medical Sciences Congress, Queenstown, New Zealand (Abstr) (Aug. 27–Aug. 29, 2012).

Long, D. S. Hargrave-Thomas, E., & Clarke, R. (2012) Stokes Flow Through a Tube Lined with a Porous Wall Layer: An Application to Microvascular Hemodynamics. 23rd International Symposium on Transport Phenomena, Auckland, New Zealand (Nov. 19–Nov. 22, 2012).

Long, D. S. & Lim, Y. (2011) An Animal Specific Approach to Quantifying the Effect of Local Hemo- dynamics on Aortic Endothelial Cell Phenotype. 2011 Medical Sciences Congress, Queenstown, New Zealand (Abstr) (Aug. 29–Aug. 21, 2011).

Lim, Y. & Long, D. S. (2011) Aortic Heamodynamics and Endothelial Gene Expression: An Animal Specific Approach. 2011 ASME Summer Bioengineering Conference, June 22–25, 2011, Famington, Pennsylvania, USA.

Long, D. S. & Lim, Y. (2010) Regional Hemodynamic Determinants of Arterial Endothelial Phenotype. 2010 Medical Sciences Congress, Queenstown, New Zealand (Abstr) (Nov. 30–Dec. 3, 2010).

Long, D. S., Nohejl, C. & Friedman, M. H. (2008) Laser Capture Microdissection of Murine Coronary En- dothelial Cells Guided by Lectin Labeling 2008 Annual Meeting of the Biomedical Engineering Society, St. Louis, MO. (Abstr) (Oct. 2–4, 2008).

Long, D. S., Zhu, H. & Friedman, M. H. (2008) Quantifying the Motion of Murine Epicardial Coronary Arteries 2008 ASME Summer Bioengineering Conference

Long, D. S., Zhu, H., & Friedman, M. H. (2007) Dynamic imaging and 3-D reconstruction of the motion of murine epicardial coronary arteries in vivo. 2007 Annual Meeting of the Biomedical Engineering Society, Los Angeles, CA. (Abstr).

Zhu, H., Shih, J., Long, D. S., Maeda, N. N., Hagaman, J. R., & Friedman, M. H. (2007) Different Strains of Mice Exhibit Different Aortic Arch Geometry and Plaque Distribution: A Fluid Dynamic Effect? 2007 ASME Summer Bioengineering Conference

Long, D. S., Zhu, H., & Friedman, M. H. (2006) Dynamic imaging and 3-D reconstruction of the motion of murine epicardial coronary arteries in vivo. 2006 Annual Meeting of the Biomedical Engineering Society, Chicago, IL. (Abstr).

Zhu, H., Shih, J., Long, D. S., Maeda, N. N., Hagaman, J. R., & Friedman, M. H. (2006) Characterizing 3-D Geometry of Mouse Aorta Arch Using Light Stereo-Microscopic Imaging. 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Conference, New York, New York, 385– 388.

Long, D. S., Zhu, H., & Friedman, M. H. (2006) A stereo-microscope based imaging system to reconstruct the 3-D motion of murine coronary arteries. NIH National Institute of Biomedical Imaging and Bio- engineering T-32 Grantee Meeting, June 16, 2006, Washington Court Hotel, Washington D.C. (Abstr).

Long, D. S., Smith, M. L., Ley, K. & Damiano, E. R. (2003) Estimation of cross-sectional viscosity and hematocrit profiles and other rheological parameters in venules using intravital fluorescent micro- particle image velocimetry. FASEB J., 18 (Abstr).

Long, D. S., Smith, M. L., Pries, A. R., Ley, K. & Damiano, E. R. (2004) Micro-viscometry reveals reduced blood viscosity in microvessels after isovolemic hemodilution. Ann. Biomed. Eng. (Abstr).

Long, D. S., Smith, M. L., Ley, K., & Damiano, E. R. (2004) Micro-viscometry predicts distributions in blood viscosity, shear rate, and shear stress in microvessels in vivo. 21st Annual Houston Conference on Biomedical Engineering Research.

Long, D. S., Smith, M. L., Ley, K., Pries, A. R. & Damiano, E. R. (2003) A micro-viscometric method predicts viscosity and hematocrit profiles in venules using μ-PIV. Ann. Biomed. Eng.

Long, D. S., Smith, M. L., Ley, K., Pries, A. R. & Damiano, E. R. (2003) Microhemofluidics in post- capillary venules determined from fluorescent intravital micro-particle image velocimetry. Proceedings of the 2003 Bioengineering Conference, ASME BED.

Smith, M. L., Long, D. S., Damiano, E. R., & Ley, K. (2003) High-resolution near-wall fluorescent micro- particle image velocimetry reveals the presence of a hemodynamically relevant endothelial surface layer in microvessels in vivo. Proceedings of the 2003 Bioengineering Conference, ASME BED.

Long, D. S., Smith, M. L., Ley, K., Pries, A. R. & Damiano, E. R. (2003) Estimation of cross-sectional vis- cosity and hematocrit profiles and other rheological parameters in smooth glass tubes using fluorescent micro-particle image velocimetry. FASEB J., 17, A100.21 (Abstr).

Smith, M. L., Long, D. S., Damiano, E. R. & Ley, K. (2003) High-resolution near-wall fluorescent micro- particle image velocimetry reveals the presence of a hemodynamically relevant endothelial surface layer in microvessels in vivo. FASEB J., 17, A100.22 (Abstr).

Long, D. S., Smith, M. L., Ley, K. & Damiano, E. R. (2002) Theoretical and experimental investigations into the motion of neutrally buoyant microspheres in the plasma-rich layer of venules. FASEB J., 16, A413.3 (Abstr).

Long, D. S., Smith, M. L., Ley, K. & Damiano, E. R. (2002) A semi-empirical approach to determining the cross-sectional viscosity distribution and other rheological parameters in vivo. FASEB J., 16, A413.6 (Abstr).

Smith, M. L., Long, D. S., Damiano, E. R. & Ley, K. (2002) Evidence for an endothelial-cell glycocalyx layer from high-resolution velocity profiles measured in venules in vivo. FASEB J., 16, A413.4 (Abstr).

Long, D. S., Smith, M. L., Ley, K. & Damiano, E. R. (2001) Flow of microspheres in the plasma layer of venules: theory versus experiment. Ann. Biomed. Eng., 29, Supp. 1, S-27 (Abstr).

Smith, M. L., Long, D. S., Damiano, E. R. & Ley, K. (2001) Experimental and theoretical analysis of shear rate and apparent viscosity of blood flow in venules. Ann. Biomed. Eng., 29, Supp. 1, S-73.5 (Abstr).

Long, D. S., Shannon, M. A, & Aluru, N. (2000) A novel approach for determining pull-in voltages in micro-electro-mechanical systems (MEMS). Technical Proceedings of the 3rd International Conference on Modeling and Simulation of Microsystems (MSM2000), 3, Ch. 11, 481-484.

Long, D. S., Aluru, N. & Shannon, M. A. (1999) A hybrid finite-element/boundary element method for two-dimensional modeling of coupled electro-mechanical devices. 5th U.S. National Congress on Com- putational Mechanics. p 231-232, August 4-6, 1999.