المؤلفون: Wong, Alexander, Lin, Zhong Qiu, Wang, Linda, Chung, Audrey G., Shen, Beiyi, Abbasi, Almas, Hoshmand-Kochi, Mahsa, Duong, Timothy Q.

مصطلحات موضوعية: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning

الوصف: Background: A critical step in effective care and treatment planning for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the COVID-19 pandemic, is the assessment of the severity of disease progression. Chest x-rays (CXRs) are often used to assess SARS-CoV-2 severity, with two important assessment metrics being extent of lung involvement and degree of opacity. In this proof-of-concept study, we assess the feasibility of computer-aided scoring of CXRs of SARS-CoV-2 lung disease severity using a deep learning system. Materials and Methods: Data consisted of 396 CXRs from SARS-CoV-2 positive patient cases. Geographic extent and opacity extent were scored by two board-certified expert chest radiologists (with 20+ years of experience) and a 2nd-year radiology resident. The deep neural networks used in this study, which we name COVID-Net S, are based on a COVID-Net network architecture. 100 versions of the network were independently learned (50 to perform geographic extent scoring and 50 to perform opacity extent scoring) using random subsets of CXRs from the study, and we evaluated the networks using stratified Monte Carlo cross-validation experiments. Findings: The COVID-Net S deep neural networks yielded R$^2$ of 0.664 $\pm$ 0.032 and 0.635 $\pm$ 0.044 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively, in stratified Monte Carlo cross-validation experiments. The best performing networks achieved R$^2$ of 0.739 and 0.741 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively. Interpretation: The results are promising and suggest that the use of deep neural networks on CXRs could be an effective tool for computer-aided assessment of SARS-CoV-2 lung disease severity, although additional studies are needed before adoption for routine clinical use.
Comment: 8 pages

الوصول الحر: http://arxiv.org/abs/2005.12855Test

المؤلفون: Jiang, Zhao, Chernoff, Diane, Galenchik-Chan, Andre, Tomorr, David, Honkanen, Robert A., Duong, Timothy Q., Muir, Eric R.

المصدر: Frontiers in Ophthalmology; 2024, p1-14, 14p

المؤلفون: Li, Wei, Liu, Chunlei, Duong, Timothy Q, Zijl, Peter CM, Li, Xu

المصدر: NMR in Biomedicine. 30(4)

مصطلحات موضوعية: Engineering, Biomedical Engineering, Biomedical Imaging, Brain Disorders, Neurosciences, Bioengineering, Animals, Brain, Diffusion Tensor Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Neuroimaging, Reproducibility of Results, Sensitivity and Specificity, White Matter, brain imaging, white matter, gradient echo MRI, phase contrast, quantitative susceptibility mapping, susceptibility tensor imaging, fiber tracking, Medicinal and Biomolecular Chemistry, Clinical Sciences, Nuclear Medicine & Medical Imaging, Clinical sciences, Biomedical engineering

الوصف: Susceptibility tensor imaging (STI) is a recently developed MRI technique that allows quantitative determination of orientation-independent magnetic susceptibility parameters from the dependence of gradient echo signal phase on the orientation of biological tissues with respect to the main magnetic field. By modeling the magnetic susceptibility of each voxel as a symmetric rank-2 tensor, individual magnetic susceptibility tensor elements as well as the mean magnetic susceptibility and magnetic susceptibility anisotropy can be determined for brain tissues that would still show orientation dependence after conventional scalar-based quantitative susceptibility mapping to remove such dependence. Similar to diffusion tensor imaging, STI allows mapping of brain white matter fiber orientations and reconstruction of 3D white matter pathways using the principal eigenvectors of the susceptibility tensor. In contrast to diffusion anisotropy, the main determinant factor of the susceptibility anisotropy in brain white matter is myelin. Another unique feature of the susceptibility anisotropy of white matter is its sensitivity to gadolinium-based contrast agents. Mechanistically, MRI-observed susceptibility anisotropy is mainly attributed to the highly ordered lipid molecules in the myelin sheath. STI provides a consistent interpretation of the dependence of phase and susceptibility on orientation at multiple scales. This article reviews the key experimental findings and physical theories that led to the development of STI, its practical implementations, and its applications for brain research. Copyright © 2016 John Wiley & Sons, Ltd.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/47n703t7Test

المؤلفون: Jiang, Zhao, Chernoff, Diane, Galenchik-Chan, Andre, Tomorri, David, Honkanen, Robert A., Duong, Timothy Q., Muir, Eric R.

المصدر: Frontiers in Ophthalmology, 4

مصطلحات موضوعية: Choroid, MRI, Glaucoma, imaging, Blood flow, Retina, Mouse

الوصف: Purpose: Blood flow (BF) of the retinal and choroidal vasculatures can be quantitatively imaged using MRI. This study sought to improve methods of data acquisition and analysis for MRI of layer-specific retinal and choroidal BF and then applied this approach to detect reduced ocular BF in a well-established mouse model of glaucoma from both eyes. Methods: Quantitative BF magnetic resonance imaging (MRI) was performed on glaucomatous DBA/2J and normal C57BL/6J mice. Arterial spin labeling MRI was applied to image retinal and choroidal BF using custom-made dual eye coils that could image both eyes during the same scan. Statistics using data from a single eye or two eyes were compared. BF values were calculated using two approaches. The BF rate per quantity of tissue was calculated as commonly done, and the peak BF values of the retinal and choroidal vasculatures were taken. Additionally, the BF rate per retinal surface area was calculated using a new analysis approach to attempt to reduce partial volume and variability by integrating BF over the retinal and choroidal depths. Results: Ocular BF of both eyes could be imaged using the dual coil setup without effecting scan time. Intraocular pressure was significantly elevated in DBA/2J mice compared to C57BL/6J mice (P<0.01). Both retinal and choroidal BF were significantly decreased in DBA/2J mice in comparison to the age-matched normal C57BL/6J mice across all measurements (P < 0.01). From simulations, the values from the integrated BF analysis method had less partial volume effect, and from in vivo scans, this analysis approach also improved power. Conclusion: The dual eye coil setup allows bilateral eye data acquisition, increasing the amount of data acquired without increasing acquisition times in vivo. The reduced ocular BF found using the improved acquisition and analysis approaches replicated the results of previous studies on DBA/2J mice. The ocular hypertensive stress-induced BF reduction found within these mice may represent changes associated with ...

العلاقة: https://doi.org/10.17615/40pd-x688Test; https://cdr.lib.unc.edu/downloads/6108vp234?file=thumbnailTest; https://cdr.lib.unc.edu/downloads/6108vp234Test

الإتاحة: https://doi.org/10.17615/40pd-x688Test
https://cdr.lib.unc.edu/downloads/6108vp234?file=thumbnailTest
https://cdr.lib.unc.edu/downloads/6108vp234Test

المؤلفون: Karagiannis, George S., Bianchi, Anthony, Sanchez, Luis Rivera, Ambadipudi, Kamal, Cui, Min-Hui, Anampa, Jesus M., Asiry, Saeed, Wang, Yarong, Harney, Allison S., Pastoriza, Jessica M., Lin, Yu, Chen, Xiaoming, Jones, Joan G., Entenberg, David, Haddad, Dana, Hodges, Laura J., Duong, Timothy Q., Sparano, Joseph A., Oktay, Maja H., Branch, Craig A., Condeelis, John S.

المصدر: npj Breast Cancer ; volume 8, issue 1 ; ISSN 2374-4677

مصطلحات موضوعية: Pharmacology (medical), Radiology, Nuclear Medicine and imaging, Oncology

الوصف: Metastatic dissemination in breast cancer is regulated by specialized intravasation sites called “tumor microenvironment of metastasis” (TMEM) doorways, composed of a tumor cell expressing the actin-regulatory protein Mena, a perivascular macrophage, and an endothelial cell, all in stable physical contact. High TMEM doorway number is associated with an increased risk of distant metastasis in human breast cancer and mouse models of breast carcinoma. Here, we developed a novel magnetic resonance imaging (MRI) methodology, called TMEM Activity-MRI , to detect TMEM-associated vascular openings that serve as the portal of entry for cancer cell intravasation and metastatic dissemination. We demonstrate that TMEM Activity-MRI correlates with primary tumor TMEM doorway counts in both breast cancer patients and mouse models, including MMTV-PyMT and patient-derived xenograft models. In addition, TMEM Activity-MRI is reduced in mouse models upon treatment with rebastinib, a specific and potent TMEM doorway inhibitor. TMEM Activity-MRI is an assay that specifically measures TMEM-associated vascular opening (TAVO) events in the tumor microenvironment, and as such, can be utilized in mechanistic studies investigating molecular pathways of cancer cell dissemination and metastasis. Finally, we demonstrate that TMEM Activity-MRI increases upon treatment with paclitaxel in mouse models, consistent with prior observations that chemotherapy enhances TMEM doorway assembly and activity in human breast cancer. Our findings suggest that TMEM Activity-MRI is a promising precision medicine tool for localized breast cancer that could be used as a non-invasive test to determine metastatic risk and serve as an intermediate pharmacodynamic biomarker to monitor therapeutic response to agents that block TMEM doorway-mediated dissemination.

الإتاحة: https://doi.org/10.1038/s41523-022-00463-5Test
https://www.nature.com/articles/s41523-022-00463-5.pdfTest
https://www.nature.com/articles/s41523-022-00463-5Test

المؤلفون: Muir, Eric R., Chandra, Saurav B., Narayanan, Divya, Zhang, Vincent, Zhang, Ike, Jiang, Zhao, Kiel, Jeffrey W., Duong, Timothy Q.

المساهمون: Badea, Tudor C., National Eye Institute, National Institutes of Health

المصدر: PLOS ONE ; volume 17, issue 3, page e0266192 ; ISSN 1932-6203

الوصف: Purpose To test the hypothesis that mild chronic hyperoxia treatment would improve retinal function despite a progressive decline in ocular blood flow in the DBA/2J mouse model of glaucoma. Materials and methods DBA/2J mice were treated with chronic mild hyperoxia (30% O 2 ) beginning at 4.5 months of age or were untreated by giving normal room air. Retinal and choroidal blood flow (RBF and ChBF, respectively) were measured at 4, 6, and 9 months of age by MRI. Blood flow was additionally measured under hypercapnia challenge (5% CO 2 inhalation) to assess vascular reactivity. Intraocular pressure (IOP) was measured using a rebound tonometer at the same time points. Scotopic flash electroretinograms (ERGs) were recorded at 9 months of age. Results Both ChBF and RBF were reduced and significantly affected by age (p < 0.01), but neither were significantly affected by O 2 -treatment (p > 0.05). ChBF significantly increased in response to hypercapnia (p < 0.01), which was also unaffected by O 2 -treatment. Significant effects of age (p < 0.001) and of the interaction of age with treatment (p = 0.028) were found on IOP. IOP significantly decreased in O 2 -treated mice at 6 months compared to 4 months of age (p < 0.001), while IOP trended to increase with age in untreated mice. The amplitude of the b-wave from ERG was significantly increased in O 2 -treated DBA/2J compared to the untreated mice (p = 0.012), while the a-wave and oscillatory potentials were not significantly affected (p > 0.05). Conclusion This study investigated the effects of chronic mild hyperoxia on retinal function and on retinal and choroidal blood flow in a mouse model of glaucoma. Retinal function was improved in the O 2 -treated mice at late stage, despite a progressive decline of RBF and ChBF with age that was comparable to untreated mice.

الإتاحة: https://doi.org/10.1371/journal.pone.0266192Test

المؤلفون: Li, Wei, Wang, Nian, Yu, Fang, Han, Hui, Cao, Wei, Romero, Rebecca, Tantiwongkosi, Bundhit, Duong, Timothy Q, Liu, Chunlei

مصطلحات موضوعية: Bioengineering, Biomedical Imaging, Brain Disorders, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Adult, Algorithms, Artifacts, Brain, Brain Mapping, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Multiple Sclerosis, Quantitative susceptibility mapping, Streaking artifact removal, Multiple sclerosis, High resolution brain imaging, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery

الوصف: Quantitative susceptibility mapping (QSM) is a novel MRI method for quantifying tissue magnetic property. In the brain, it reflects the molecular composition and microstructure of the local tissue. However, susceptibility maps reconstructed from single-orientation data still suffer from streaking artifacts which obscure structural details and small lesions. We propose and have developed a general method for estimating streaking artifacts and subtracting them from susceptibility maps. Specifically, this method uses a sparse linear equation and least-squares (LSQR)-algorithm-based method to derive an initial estimation of magnetic susceptibility, a fast quantitative susceptibility mapping method to estimate the susceptibility boundaries, and an iterative approach to estimate the susceptibility artifact from ill-conditioned k-space regions only. With a fixed set of parameters for the initial susceptibility estimation and subsequent streaking artifact estimation and removal, the method provides an unbiased estimate of tissue susceptibility with negligible streaking artifacts, as compared to multi-orientation QSM reconstruction. This method allows for improved delineation of white matter lesions in patients with multiple sclerosis and small structures of the human brain with excellent anatomical details. The proposed methodology can be extended to other existing QSM algorithms.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/1sp2j3ngTest

المؤلفون: Park, Sung-Hong, Wang, Danny JJ, Duong, Timothy Q

المصدر: Magnetic resonance imaging. 31(7)

مصطلحات موضوعية: Kidney, Arteries, Brain, Visual Cortex, Retina, Humans, Spin Labels, Contrast Media, Magnetic Resonance Imaging, Blood Flow Velocity, Artifacts, Perfusion, Cerebrovascular Circulation, Algorithms, Image Processing, Computer-Assisted, Arterial spin labeling, Balanced steady state free precession, Blood flow, Pseudo-continuous arterial spin labeling, fMRI, Nuclear Medicine & Medical Imaging, Biomedical Engineering, Clinical Sciences, Cognitive Sciences

الوصف: We implemented pseudo-continuous ASL (pCASL) with 2D and 3D balanced steady state free precession (bSSFP) readout for mapping blood flow in the human brain, retina, and kidney, free of distortion and signal dropout, which are typically observed in the most commonly used echo-planar imaging acquisition. High resolution functional brain imaging in the human visual cortex was feasible with 3D bSSFP pCASL. Blood flow of the human retina could be imaged with pCASL and bSSFP in conjunction with a phase cycling approach to suppress the banding artifacts associated with bSSFP. Furthermore, bSSFP based pCASL enabled us to map renal blood flow within a single breath hold. Control and test-retest experiments suggested that the measured blood flow values in retina and kidney were reliable. Because there is no specific imaging tool for mapping human retina blood flow and the standard contrast agent technique for mapping renal blood flow can cause problems for patients with kidney dysfunction, bSSFP based pCASL may provide a useful tool for the diagnosis of retinal and renal diseases and can complement existing imaging techniques.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/0qs884jwTest

المؤلفون: Muir, Eric R., Narayanan, Divya, Chandra, Saurav B., Akimov, Nikolay P., Sohn, Jeong-Hyeon, Meyer, Evan, Rentería, René C., Duong, Timothy Q.

المساهمون: Badea, Tudor C., National Center for Advancing Translational Sciences, biogen, calyx, National Eye Institute, Semp Russ Foundation and Lila G. and Dessey F. Taylor Fund of the San Antonio Area Foundation, IIMS/CTSA Translational Technology Award, IIMS/CTSA Center for Biomedical Neuroscience Pilot Project Award

المصدر: PLOS ONE ; volume 16, issue 12, page e0259505 ; ISSN 1932-6203

الوصف: Purpose The purpose of this study was to investigate neuronal and vascular functional deficits in the retina and their association in a diabetic mouse model. We measured electroretinography (ERG) responses and choroidal and retinal blood flow (ChBF, RBF) with magnetic resonance imaging (MRI) in healthy and diabetic mice under basal conditions and under hypercapnic challenge. Methods Ins2 Akita diabetic (Diab, n = 8) and age-matched, wild-type C57BL/6J mice (Ctrl, n = 8) were studied under room air and moderate hypercapnia (5% CO 2 ). Dark-adapted ERG a-wave, b-wave, and oscillatory potentials (OPs) were measured for a series of flashes. Regional ChBF and RBF under air and hypercapnia were measured using MRI in the same mice. Results Under room air, Diab mice had compromised ERG b-wave and OPs (e.g., b-wave amplitude was 422.2±10.7 μV in Diab vs. 600.1±13.9 μV in Ctrl, p < 0.001). Under hypercapnia, OPs and b-wave amplitudes were significantly reduced in Diab (OPs by 30.3±3.0% in Diab vs. -3.0±3.6% in Ctrl, b-wave by 17.9±1.4% in Diab vs. 1.3±0.5% in Ctrl). Both ChBF and RBF had significant differences in regional blood flow, with Diab mice having substantially lower blood flow in the nasal region (ChBF was 5.4±1.0 ml/g/min in Diab vs. 8.6±1.0 ml/g/min in Ctrl, RBF was 0.91±0.10 ml/g/min in Diab vs. 1.52±0.24 ml/g/min in Ctrl). Under hypercapnia, ChBF increased in both Ctrl and Diab without significant group difference (31±7% in Diab vs. 17±7% in Ctrl, p > 0.05), but an increase in RBF was not detected for either group. Conclusions Inner retinal neuronal function and both retinal and choroidal blood flow were impaired in Diab mice. Hypercapnia further compromised inner retinal neuronal function in diabetes, while the blood flow response was not affected, suggesting that the diabetic retina has difficulty adapting to metabolic challenges due to factors other than impaired blood flow regulation.

الإتاحة: https://doi.org/10.1371/journal.pone.0259505Test

المؤلفون: Huang, Shiliang, Shen, Qiang, Watts, Lora Talley, Long, Justin A., O'Boyle, Michael, Nguyen, Tony, Muir, Eric, Duong, Timothy Q.

المصدر: Neurotrauma Reports ; volume 2, issue 1, page 526-540 ; ISSN 2689-288X

الإتاحة: https://doi.org/10.1089/neur.2021.0023Test