Whiting School of Engineering

Research Output 1966 2019

Filter
Article
2019

2019 data fusion contest

Le Saux, B., Yokoya, N., Hansch, R., Brown, M. & Hager, G., Mar 1 2019, IEEE Geoscience and Remote Sensing Magazine, 7, 1, p. 103-105 3 p.

Research output: Contribution to specialist publicationArticle

multisensor fusion
Data fusion

A 3D Computational Head Model Under Dynamic Head Rotation and Head Extension Validated Using Live Human Brain Data, Including the Falx and the Tentorium

Lu, Y. C., Daphalapurkar, N. P., Knutsen, A. K., Glaister, J., Pham, D. L., Butman, J. A., Prince, J. L., Bayly, P. V. & Ramesh, K. T., Jan 1 2019, In : Annals of biomedical engineering.

Research output: Contribution to journalArticle

Brain
Magnetic resonance
Anisotropy
Tissue

A direct podocalyxin–dynamin-2 interaction regulates cytoskeletal dynamics to promote migration and metastasis in pancreatic cancer cells

Wong, B. S., Shea, D. J., Mistriotis, P., Tuntithavornwat, S., Law, R. A., Bieber, J. M., Zheng, L. & Konstantopoulos, K., Jun 1 2019, In : Cancer Research. 79, 11, p. 2878-2891 14 p.

Research output: Contribution to journalArticle

Pancreatic Neoplasms
Neoplasm Metastasis
Dynamin II
Microtubules
Focal Adhesions

A humanized yeast system to analyze cleavage of prelamin A by ZMPSTE24

Spear, E., Alford, R. F., Babatz, T. D., Wood, K. M., Mossberg, O. W., Odinammadu, K., Shilagardi, K., Gray, J. J. & Michaelis, S. D., Jan 1 2019, (Accepted/In press) In : Methods.

Research output: Contribution to journalArticle

Yeast
Yeasts
Processing
Lamin Type A
Aging of materials

Alterations in the retinal vasculature occur in multiple sclerosis and exhibit novel correlations with disability and visual function measures

Murphy, O. C., Kwakyi, O., Iftikhar, M., Zafar, S., Lambe, J., Pellegrini, N., Sotirchos, E. S., Gonzalez-Caldito, N., Ogbuokiri, E., Filippatou, A., Risher, H., Cowley, N., Feldman, S., Fioravante, N., Frohman, E. M., Frohman, T. C., Balcer, L. J., Prince, J. L., Channa, R., Calabresi, P. & 1 others, Saidha, S., Jan 1 2019, In : Multiple Sclerosis Journal.

Research output: Contribution to journalArticle

Multiple Sclerosis
Blood Vessels
Neuritis
Retinal Vessels
Optic Neuritis

A microfluidic assay for the quantification of the metastatic propensity of breast cancer specimens

Yankaskas, C. L., Thompson, K. N., Paul, C. D., Vitolo, M. I., Mistriotis, P., Mahendra, A., Bajpai, V. K., Shea, D. J., Manto, K. M., Chai, A. C., Varadarajan, N., Kontrogianni-Konstantopoulos, A., Martin, S. S. & Konstantopoulos, K., Jan 1 2019, In : Nature biomedical engineering.

Research output: Contribution to journalArticle

Microfluidics
Assays
Cells
Breast Neoplasms
Neoplasm Metastasis

Applications of a deep learning method for anti-aliasing and super-resolution in MRI

Zhao, C., Shao, M., Carass, A., Li, H., Dewey, B. E., Ellingsen, L. M., Woo, J., Guttman, M. A., Blitz, A. M., Stone, M., Calabresi, P. A., Halperin, H. & Prince, J. L., Jan 1 2019, In : Magnetic Resonance Imaging.

Research output: Contribution to journalArticle

Anti-aliasing
Magnetic resonance
Magnetic resonance imaging
Magnetic Resonance Spectroscopy
Learning

Applied Force during Piston Prosthesis Placement in a 3D-Printed Model: Freehand vs Robot-Assisted Techniques

Razavi, C. R., Wilkening, P. R., Yin, R., Lamaison, N., Taylor, R. H., Carey, J. P. & Creighton, F., Feb 1 2019, In : Otolaryngology - Head and Neck Surgery (United States). 160, 2, p. 320-325 6 p.

Research output: Contribution to journalArticle

Robotics
Prostheses and Implants
Incus
Microsurgery
Stapes

Aquaporin-4 IgG seropositivity is associated with worse visual outcomes after optic neuritis than MOG-IgG seropositivity and multiple sclerosis, independent of macular ganglion cell layer thinning

Sotirchos, E. S., Filippatou, A., Fitzgerald, K. C., Salama, S., Pardo, S., Wang, J., Ogbuokiri, E., Cowley, N. J., Pellegrini, N., Murphy, O. C., Mealy, M. A., Prince, J. L., Levy, M., Calabresi, P. A. & Saidha, S., Jan 1 2019, (Accepted/In press) In : Multiple Sclerosis Journal.

Research output: Contribution to journalArticle

Aquaporin 4
Optic Neuritis
Ganglia
Multiple Sclerosis
Myelin-Oligodendrocyte Glycoprotein

Assessment of Automated Identification of Phases in Videos of Cataract Surgery Using Machine Learning and Deep Learning Techniques

Yu, F., Silva Croso, G., Kim, T. S., Song, Z., Parker, F., Hager, G., Reiter, A., Vedula, S. S., Ali, H. & Sikder, S., Apr 5 2019, In : JAMA network open. 2, 4, p. e191860

Research output: Contribution to journalArticle

Cataract
Learning
ROC Curve
Ophthalmology
Internship and Residency

Atlas-based tongue muscle correlation analysis from tagged and high- resolution magnetic resonance imaging

Xing, F., Stone, M., Goldsmith, T., Prince, J. L., Fakhri, G. E. & Woo, J., Jul 2019, In : Journal of Speech, Language, and Hearing Research. 62, 7, p. 2258-2269 12 p.

Research output: Contribution to journalArticle

Atlases
Tongue
Magnetic Resonance Imaging
Muscles
Mouth Floor

Automated detection & classification of knee arthroplasty using deep learning

Yi, P. H., Wei, J., Kim, T. K., Sair, H. I., Hui, F. K., Hager, G. D., Fritz, J. & Oni, J. K., Jan 1 2019, (Accepted/In press) In : Knee.

Research output: Contribution to journalArticle

Knee Replacement Arthroplasties
Learning
Area Under Curve
Knee
Arthroplasty

Automated semantic labeling of pediatric musculoskeletal radiographs using deep learning

Yi, P. H., Kim, T. K., Wei, J., Shin, J., Hui, F., Sair, H., Hager, G. & Fritz, J., Jan 1 2019, In : Pediatric radiology.

Research output: Contribution to journalArticle

Semantics
Learning
Pediatrics
ROC Curve
Area Under Curve

Brain ventricle parcellation using a deep neural network: Application to patients with ventriculomegaly

Shao, M., Han, S., Carass, A., Li, X., Blitz, A. M., Shin, J., Prince, J. L. & Ellingsen, L. M., Jan 1 2019, In : NeuroImage: Clinical. 23, 101871.

Research output: Contribution to journalArticle

Open Access
Brain
Normal Pressure Hydrocephalus
Brain Diseases
Hydrocephalus
Cerebrospinal Fluid

Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation

Santiago-Frangos, A., Fröhlich, K. S., Jeliazkov, J. R., Małecka, E. M., Marino, G., Gray, J. J., Luisi, B. F., Woodson, S. A. & Hardwick, S. W., May 28 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 166, 22, p. 10978-10987 10 p.

Research output: Contribution to journalArticle

Open Access
Caulobacter crescentus
RNA
Alphaproteobacteria
Substrate Specificity
Protein C

Cell sensing and decision-making in confinement: The role of TRPM7 in a tug of war between hydraulic pressure and cross-sectional area

Zhao, R., Afthinos, A., Zhu, T., Mistriotis, P., Li, Y., Serra, S. A., Zhang, Y., Yankaskas, C. L., He, S., Valverde, M. A., Sun, S. X. & Konstantopoulos, K., Jul 24 2019, In : Science Advances. 5, 7, eaaw7243.

Research output: Contribution to journalArticle

Open Access
decision making
hydraulics
cells
microchannels
myosins

Comparison of Automated Activity Recognition to Provider Observations of Patient Mobility in the ICU

Rawat, N., Rao, V., Peven, M., Shrock, C., Reiter, A., Saria, S. & Ali, H., Sep 1 2019, In : Critical care medicine. 47, 9, p. 1232-1234 3 p.

Research output: Contribution to journalArticle

Surgical Instruments
Documentation
Caregivers
Observational Studies
Nurses

Computer-based engineering of thermostabilized antibody fragments

Lee, J., Der, B. S., Karamitros, C. S., Li, W., Marshall, N. M., Lungu, O. I., Miklos, A. E., Xu, J., Kang, T. H., Lee, C. H., Tan, B., Hughes, R. A., Jung, S. T., Ippolito, G. C., Gray, J. J., Zhang, Y., Kuhlman, B., Georgiou, G. & Ellington, A. D., Jan 1 2019, (Accepted/In press) In : AIChE Journal. e16864.

Research output: Contribution to journalArticle

Immunoglobulin Fragments
Antibodies
Amino acids
Hot Temperature
Clostridium botulinum

Confinement hinders motility by inducing RhoA-mediated nuclear influx, volume expansion, and blebbing

Mistriotis, P., Wisniewski, E. O., Bera, K., Keys, J., Li, Y., Tuntithavornwat, S., Law, R. A., Perez-Gonzalez, N. A., Erdogmus, E., Zhang, Y., Zhao, R., Sun, S. X., Kalab, P., Lammerding, J. & Konstantopoulos, K., Dec 2 2019, In : The Journal of cell biology. 218, 12, p. 4093-4111 19 p.

Research output: Contribution to journalArticle

Open Access
Blister
Myosin Type II
Nuclear Envelope
Cell Movement
Rupture

DeepHarmony: A deep learning approach to contrast harmonization across scanner changes

Dewey, B. E., Zhao, C., Reinhold, J. C., Carass, A., Fitzgerald, K. C., Sotirchos, E. S., Saidha, S., Oh, J., Pham, D. L., Calabresi, P. A., van Zijl, P. C. M. & Prince, J. L., Jan 1 2019, In : Magnetic Resonance Imaging.

Research output: Contribution to journalArticle

Magnetic resonance imaging
Magnetic Resonance Imaging
Learning
Atrophy
Hardware

Deep-Learning-Based Semantic Labeling for 2D Mammography and Comparison of Complexity for Machine Learning Tasks

Yi, P. H., Lin, A., Wei, J., Yu, A. C., Sair, H., Hui, F., Hager, G. & Harvey, S., Jan 1 2019, In : Journal of Digital Imaging.

Research output: Contribution to journalArticle

Open Access
Mammography
Semantics
Labeling
Learning systems
Learning

Deep Learning Method for Automated Classification of Anteroposterior and Posteroanterior Chest Radiographs

Kim, T. K., Yi, P. H., Wei, J., Shin, J. W., Hager, G., Hui, F., Sair, H. & Lin, C., Jan 1 2019, (Accepted/In press) In : Journal of Digital Imaging.

Research output: Contribution to journalArticle

Pediatrics
Thorax
Learning
Neural networks
Learning systems

Differentiating post-cancer from healthy tongue muscle coordination patterns during speech using deep learning

Woo, J., Xing, F., Prince, J. L., Stone, M., Green, J. R., Goldsmith, T., Reese, T. G., Wedeen, V. J. & El Fakhri, G., May 1 2019, In : Journal of the Acoustical Society of America. 145, 5, p. EL423-EL429

Research output: Contribution to journalArticle

Open Access
tongue
muscles
learning
magnetic resonance
cancer
Vascular Endothelial Growth Factor Receptor-2
Dimerization
Ligands
Vascular Endothelial Growth Factor A
Human Development

Do no harm: a roadmap for responsible machine learning for health care

Wiens, J., Saria, S., Sendak, M., Ghassemi, M., Liu, V. X., Doshi-Velez, F., Jung, K., Heller, K., Kale, D., Saeed, M., Ossorio, P. N., Thadaney-Israni, S. & Goldenberg, A., Jan 1 2019, (Accepted/In press) In : Nature medicine.

Research output: Contribution to journalArticle

Open Access
Health care
Learning systems
Delivery of Health Care
Medicine
Patient Care

Dose/Volume histogram patterns in Salivary Gland subvolumes influence xerostomia injury and recovery

Han, P., Lakshminarayanan, P., Jiang, W., Shpitser, I., Hui, X., Lee, S. H., Cheng, Z., Guo, Y., Taylor, R. H., Siddiqui, S. A., Bowers, M., Sheikh, K., Kiess, A. P., Page, B., Lee, J., Quon, H. & McNutt, T., Dec 1 2019, In : Scientific reports. 9, 1, 3616.

Research output: Contribution to journalArticle

Open Access
Xerostomia
Salivary Glands
Wounds and Injuries
Radiotherapy
Mouth

Effect of disease-modifying therapies on subcortical gray matter atrophy in multiple sclerosis

Sotirchos, E. S., Gonzalez-Caldito, N., Dewey, B. E., Fitzgerald, K., Glaister, J., Filippatou, A., Ogbuokiri, E., Feldman, S., Kwakyi, O., Risher, H., Crainiceanu, C. M., Pham, D. L., Van Zijl, P. C., Mowry, E. M., Reich, D. S., Prince, J. L., Calabresi, P. & Saidha, S., Jan 1 2019, In : Multiple Sclerosis Journal.

Research output: Contribution to journalArticle

Multiple Sclerosis
Atrophy
Therapeutics
Brain
Gray Matter

Enabling machine learning in X-ray-based procedures via realistic simulation of image formation

Unberath, M., Zaech, J. N., Gao, C., Bier, B., Goldmann, F., Lee, S. C., Fotouhi, J., Taylor, R. H., Armand, M. & Navab, N., Jan 1 2019, In : International Journal of Computer Assisted Radiology and Surgery.

Research output: Contribution to journalArticle

Learning systems
Image processing
X-Rays
Neural networks
X rays
Tomography
Navigation
Imaging techniques
Statistics
Endoscopy

Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling

Gomez-Soler, M., Gehring, M. P., Lechtenberg, B. C., Zapata-Mercado, E., Hristova, K. A. & Pasquale, E. B., Jan 1 2019, In : Journal of Biological Chemistry. 294, 22, p. 8791-8805 15 p.

Research output: Contribution to journalArticle

varespladib methyl
Ligands
Peptides
Ephrins
Crystal structure

Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes

Roy Burman, S. S., Yovanno, R. A. & Gray, J. J., Jun 4 2019, In : Structure. 27, 6, p. 1041-1051.e8

Research output: Contribution to journalArticle

Open Access
Benchmarking
Proteins

Image-Guided Mastoidectomy with a Cooperatively Controlled ENT Microsurgery Robot

Razavi, C. R., Wilkening, P. R., Yin, R., Barber, S. R., Taylor, R. H., Carey, J. P. & Creighton, F., Jan 1 2019, (Accepted/In press) In : Otolaryngology - Head and Neck Surgery (United States).

Research output: Contribution to journalArticle

Microsurgery
Robotics
Temporal Bone
Otolaryngology
Feasibility Studies

Layer boundary evolution method for macular OCT layer segmentation

Liu, Y., Carass, A., He, Y., Antony, B. J., Filippatou, A., Saidha, S., Solomon, S., Calabresi, P. & Prince, J. L., Mar 1 2019, In : Biomedical Optics Express. 10, 3, p. 1064-1080 17 p., 349227.

Research output: Contribution to journalArticle

Optical Coherence Tomography
boundary layers
tomography
retina
evaluation

Machine Learning Methods Uncover Radiomorphologic Dose Patterns in Salivary Glands that Predict Xerostomia in Patients with Head and Neck Cancer

Jiang, W., Lakshminarayanan, P., Hui, X., Han, P., Cheng, Z., Bowers, M., Shpitser, I., Siddiqui, S., Taylor, R. H., Quon, H. & McNutt, T., Jan 1 2019, (Accepted/In press) In : Advances in Radiation Oncology.

Research output: Contribution to journalArticle

Xerostomia
Head and Neck Neoplasms
Salivary Glands
Parotid Gland
Submandibular Gland

Mechanism of Action of Peptides That Cause the pH-Triggered Macromolecular Poration of Lipid Bilayers

Kim, S. Y., Pittman, A. E., Zapata-Mercado, E., King, G. M., Wimley, W. C. & Hristova, K. A., Apr 24 2019, In : Journal of the American Chemical Society. 141, 16, p. 6706-6718 13 p.

Research output: Contribution to journalArticle

Lipid bilayers
Lipid Bilayers
Peptides
Membranes
Physical Chemistry

Myosin IIB assembly state determines its mechanosensitive dynamics

Schiffhauer, E. S., Ren, Y., Iglesias, V. A., Kothari, P., Iglesias, P. A. & Robinson, D., Mar 1 2019, In : Journal of Cell Biology. 218, 3, p. 895-908 14 p.

Research output: Contribution to journalArticle

Open Access
Nonmuscle Myosin Type IIB
Myosin Type II
NIH 3T3 Cells
Dictyostelium
Cell Shape

Non-H3 CDR template selection in antibody modeling through machine learning

Long, X., Jeliazkov, J. R. & Gray, J. J., Jan 1 2019, In : PeerJ. 2019, 1, e6179.

Research output: Contribution to journalArticle

artificial intelligence
Learning systems
antibodies
Antibodies
Immune system

Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45

Roy Burman, S. S., Nance, M. L., Jeliazkov, J. R., Labonte, J. W., Lubin, J. H., Biswas, N. & Gray, J. J., Jan 1 2019, (Accepted/In press) In : Proteins: Structure, Function and Bioinformatics.

Research output: Contribution to journalArticle

Oligosaccharides
Sampling
Proteins
Research Design
Carbohydrates

Objective assessment of intraoperative technical skill in capsulorhexis using videos of cataract surgery

Kim, T. S., O’Brien, M., Zafar, S., Hager, G., Sikder, S. & Vedula, S. S., Jan 1 2019, In : International Journal of Computer Assisted Radiology and Surgery.

Research output: Contribution to journalArticle

Capsulorhexis
Optical flows
Ophthalmology
Cataract
Surgery

Parallel deep neural networks for endoscopic oct image segmentation

Li, D., Wu, J., He, Y., Yao, X., Yuan, W., Chen, D., Park, H. C., Yu, S., Prince, J. L. & Li, X., Mar 1 2019, In : Biomedical Optics Express. 10, 3, p. 1126-1135 10 p., #349139.

Research output: Contribution to journalArticle

Eosinophilic Esophagitis
Esophagus
esophagus
Guinea Pigs
guinea pigs

Phase Image Texture Analysis for Motion Detection in Diffusion MRI (PITA-MDD)

Elsaid, N. M. H., Prince, J. L., Roys, S., Gullapalli, R. P. & Zhuo, J., Oct 2019, In : Magnetic Resonance Imaging. 62, p. 228-241 14 p.

Research output: Contribution to journalArticle

Image texture
Diffusion Magnetic Resonance Imaging
Magnetic resonance imaging
Imaging techniques
Fibers

Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease

Høydahl, L. S., Richter, L., Frick, R., Snir, O., Gunnarsen, K. S., Landsverk, O. J. B., Iversen, R., Jeliazkov, J. R., Gray, J. J., Bergseng, E., Foss, S., Qiao, S. W., Lundin, K. E. A., Jahnsen, J., Jahnsen, F. L., Sandlie, I., Sollid, L. M. & Løset, G. Å., Apr 1 2019, In : Gastroenterology. 156, 5, p. 1428-1439.e10

Research output: Contribution to journalArticle

Glutens
Celiac Disease
Plasma Cells
Peptides
Neuroglia

Pose Estimation of Periacetabular Osteotomy Fragments with Intraoperative X-Ray Navigation

Grupp, R. B., Hegeman, R., Murphy, R., Alexander, C., Otake, Y., McArthur, B., Armand, M. & Taylor, R. H., Jan 1 2019, In : IEEE Transactions on Biomedical Engineering.

Research output: Contribution to journalArticle

Navigation
Pipelines
X rays
Navigation systems
Optical systems

Quantifying Tongue Tip Shape in Apical and Laminal /s/: Contributions of Palate Shape

Stone, M., Gomez, A. D., Zhuo, J., Tchouaga, A. L. & Prince, J. L., Sep 20 2019, In : Journal of speech, language, and hearing research : JSLHR. 62, 9, p. 3149-3159 11 p.

Research output: Contribution to journalArticle

Palate
Tongue
Tooth
Magnetic Resonance Spectroscopy
Curvature

Quantitative vibratory sensation measurement is related to sensory cortical thickness in MS

Fritz, N. E., Eloyan, A., Glaister, J., Dewey, B. E., Al-Louzi, O., Costello, M. G., Chen, M., Prince, J. L., Calabresi, P. & Zackowski, K. M., Mar 1 2019, In : Annals of Clinical and Translational Neurology. 6, 3, p. 586-595 10 p.

Research output: Contribution to journalArticle

Open Access
Multiple Sclerosis
Somatosensory Cortex
Prefrontal Cortex
Brain
Hallux

Recapitulation of molecular regulators of nuclear motion during cell migration

Sneider, A., Hah, J., Wirtz, D. & Kim, D. H., Dec 1 2019, In : Cell adhesion & migration. 13, 1, p. 50-62 13 p.

Research output: Contribution to journalArticle

Open Access
Cell Movement
Cellular Microenvironment
Stress Fibers
Cell Nucleus
Organelles
Optical Coherence Tomography
Multiple Sclerosis
Retina
Germany

Revisiting a controversy: The effect of EGF on EGFR dimer stability

Singh, D. R., King, C., Salotto, M. & Hristova, K. A., Jan 1 2019, In : Biochimica et Biophysica Acta - Biomembranes.

Research output: Contribution to journalArticle

Epidermal Growth Factor
Dimers
Dimerization
Ligands
Receptor Protein-Tyrosine Kinases

Segmenting and classifying activities in robot-assisted surgery with recurrent neural networks

DiPietro, R., Ahmidi, N., Malpani, A., Waldram, M., Lee, G. I., Lee, M. R., Vedula, S. S. & Hager, G., Jan 1 2019, In : International Journal of Computer Assisted Radiology and Surgery.

Research output: Contribution to journalArticle

Gestures
Recurrent neural networks
Surgery
Biomechanical Phenomena
Robots

Spatial Radiation Dose Influence on Xerostomia Recovery and Its Comparison to Acute Incidence in Patients With Head and Neck Cancer

Guo, Y., Jiang, W., Lakshminarayanan, P., Han, P., Cheng, Z., Bowers, M., Hui, X., Shpitser, I., Siddiqui, S., Taylor, R. H., Quon, H. & McNutt, T., Jan 1 2019, (Accepted/In press) In : Advances in Radiation Oncology.

Research output: Contribution to journalArticle

Open Access
Xerostomia
Head and Neck Neoplasms
Radiation
Incidence
Radiotherapy