15 results on '"Allen Q. Ye"'
Search Results
2. BRAINtrinsic: A Virtual Reality-Compatible Tool for Exploring Intrinsic Topologies of the Human Brain Connectome.
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Giorgio Conte, Allen Q. Ye, Angus G. Forbes, Olusola Ajilore, and Alex D. Leow
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- 2015
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3. A fractal derivative model for the characterization of anomalous diffusion in magnetic resonance imaging.
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Yingjie Liang, Allen Q. Ye, Wen Chen 0003, Rodolfo G. Gatto, Luis M. Colon-Perez, Thomas H. Mareci, and Richard L. Magin
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- 2016
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4. Scattering and Diffraction of Elastodynamic Waves in a Concentric Cylindrical Phantom for MR Elastography.
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Benjamin L. Schwartz, Ziying Yin, Temel Kaya Yasar, Yifei Liu, Altaf A. Khan, Allen Q. Ye, Thomas J. Royston, and Richard L. Magin
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- 2016
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5. Diffusion tensor MRI phantom exhibits anomalous diffusion.
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Allen Q. Ye, Penny L. Hubbard Cristinacce, Fenglei Zhou, Ziying Yin, Geoffrey J. M. Parker, and Richard L. Magin
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- 2014
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6. The intrinsic geometry of the human brain connectome.
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Allen Q. Ye, Olusola Ajilore, Giorgio Conte, Johnson J. GadElkarim, Galen Thomas-Ramos, Liang Zhan, Shaolin Yang, Anand R. Kumar, Richard L. Magin, Angus Graeme Forbes, and Alex D. Leow
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- 2015
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7. Pancreatic Cystic Neoplasms
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Camila Lopes Vendrami, Allen Q. Ye, Frank H. Miller, and Paul Nikolaidis
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medicine.medical_specialty ,medicine.diagnostic_test ,Pancreas neoplasm ,business.industry ,Papillary Neoplasm ,Magnetic resonance imaging ,Mr imaging ,Imaging modalities ,Serous fluid ,medicine.anatomical_structure ,medicine ,Radiology ,Pancreas ,business ,Diffusion MRI - Abstract
With an aging population, the widespread use of cross-sectional imaging, as well as better resolution afforded by technical improvements in all imaging modalities, the detection of pancreatic cystic lesions has become quite common. Differentiation between the types of cystic lesions is critical since the malignant potential of these types of lesions varies. Serous cystic neoplasms are usually benign with no need for surveillance, whereas others like mucinous papillary neoplasms and intraductal mucinous papillary neoplasms are considered premalignant lesions requiring either surveillance or surgery. In this chapter we will discuss the general MR imaging findings of different pancreatic cystic neoplasms, along with the utility and limitations of diffusion weighted imaging (DWI) in assessing cystic lesions of the pancreas. In general, DWI may not be particularly helpful by itself in distinguishing between different cystic lesions and therefore MRI features encountered on other sequences obtained as part of a pancreatic protocol MRI will be emphasized as well. These features in conjunction with clinical and demographic data often allow for the correct diagnosis to be attained by magnetic resonance imaging.
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- 2020
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8. Detection of axonal degeneration in a mouse model of Huntington’s disease: comparison between diffusion tensor imaging and anomalous diffusion metrics
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Allen Q. Ye, Anna Lysakowski, Thomas H. Mareci, Luis M. Colon-Perez, Richard L. Magin, Gerardo Morfini, Steven D. Price, Rodolfo G. Gatto, Scott T. Brady, and M. Muge Karaman
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Male ,Anomalous diffusion ,Biophysics ,Corpus callosum ,Tortuosity ,Article ,030218 nuclear medicine & medical imaging ,Corpus Callosum ,White matter ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Nuclear magnetic resonance ,Fractional anisotropy ,medicine ,Animals ,Radiology, Nuclear Medicine and imaging ,Diffusion (business) ,Myelin Sheath ,Radiological and Ultrasound Technology ,medicine.diagnostic_test ,Chemistry ,Magnetic resonance imaging ,Magnetic Resonance Imaging ,White Matter ,Axons ,medicine.anatomical_structure ,Diffusion Tensor Imaging ,Huntington Disease ,nervous system ,Microscopy, Fluorescence ,Anisotropy ,Female ,Diffusion MRI - Abstract
OBJECTIVE: The goal of this work is to study the changes in white matter integrity in R6/2, a well-established animal model of Huntington’s disease (HD) that are captured by ex vivo diffusion imaging (DTI) using a high field MRI (17.6 T). MATERIALS AND METHODS: DTI and continuous time random walk (CTRW) models were used to fit changes in the diffusion-weighted signal intensity in the corpus callosum of controls and in R6/2 mice. RESULTS: A significant 13% decrease in fractional anisotropy, a 7% increase in axial diffusion, and a 33% increase in radial diffusion were observed between R6/2 and control mice. No change was observed in the CTRW beta parameter, but a significant decrease in the alpha parameter (− 21%) was measured. Histological analysis of the corpus callosum showed a decrease in axonal organization, myelin alterations, and astrogliosis. Electron microscopy studies demonstrated ultrastructural changes in degenerating axons, such as an increase in tortuosity in the R6/2 mice. CONCLUSIONS: DTI and CTRW diffusion models display quantitative changes associated with the microstructural alterations observed in the corpus callosum of the R6/2 mice. The observed increase in the diffusivity and decrease in the alpha CTRW parameter providing support for the use of these diffusion models for non-invasive detection of white matter alterations in HD.
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- 2019
9. Biological and MRI characterization of biomimetic ECM scaffolds for cartilage tissue regeneration
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Mrignayani Kotecha, Chun-Chieh Huang, Ziying Yin, Allen Q. Ye, Sriram Ravindran, Anne George, Richard L. Magin, and Padmabharathi Pothirajan
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Scaffold ,Materials science ,Biophysics ,Bioengineering ,Regenerative medicine ,Article ,Biomaterials ,Extracellular matrix ,Tissue engineering ,Biomimetics ,medicine ,Humans ,Cells, Cultured ,Tissue Engineering ,Tissue Scaffolds ,Cartilage ,Regeneration (biology) ,Mesenchymal stem cell ,Chondrogenesis ,Magnetic Resonance Imaging ,Extracellular Matrix ,medicine.anatomical_structure ,Mechanics of Materials ,Ceramics and Composites ,Biomedical engineering - Abstract
Osteoarthritis is the most common joint disorder affecting millions of people. Most scaffolds developed for cartilage regeneration fail due to vascularization and matrix mineralization. In this study we present a chondrogenic extracellular matrix (ECM) incorporated collagen/chitosan scaffold (chondrogenic ECM scaffold) for potential use in cartilage regenerative therapy. Biochemical characterization showed that these scaffolds possess key pro-chondrogenic ECM components and growth factors. MRI characterization showed that the scaffolds possess mechanical properties and diffusion characteristics important for cartilage tissue regeneration. In vivo implantation of the chondrogenic ECM scaffolds with bone marrow derived mesenchymal stem cells (MSCs) triggered chondrogenic differentiation of the MSCs without the need for external stimulus. Finally, results from in vivo MRI experiments indicate that the chondrogenic ECM scaffolds are stable and possess MR properties on par with native cartilage. Based on our results, we envision that such ECM incorporated scaffolds have great potential in cartilage regenerative therapy. Additionally, our validation of MR parameters with histology and biochemical analysis indicates the ability of MRI techniques to track the progress of our ECM scaffolds non-invasively in vivo; highlighting the translatory potential of this technology.
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- 2015
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10. Measuring embeddedness: Hierarchical scale-dependent information exchange efficiency of the human brain connectome
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Liang Zhan, Sean D. Conrin, Aifeng Zhang, Olusola Ajilore, Jamie D. Feusner, Shaolin Yang, Anand Kumar, Allen Q. Ye, Alex D. Leow, and Johnson GadElkarim
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Connectomics ,Theoretical computer science ,Radiological and Ultrasound Technology ,Embeddedness ,business.industry ,Modular design ,Information theory ,Neurology ,Connectome ,Graph (abstract data type) ,Radiology, Nuclear Medicine and imaging ,Neurology (clinical) ,Anatomy ,business ,Psychology ,Neuroscience ,Default mode network ,Information exchange - Abstract
This article presents a novel approach for understanding information exchange efficiency and its decay across hierarchies of modularity, from local to global, of the structural human brain connectome. Magnetic resonance imaging techniques have allowed us to study the human brain connectivity as a graph, which can then be analyzed using a graph-theoretical approach. Collectively termed brain connectomics, these sophisticated mathematical techniques have revealed that the brain connectome, like many networks, is highly modular and brain regions can thus be organized into communities or modules. Here, using tractography-informed structural connectomes from 46 normal healthy human subjects, we constructed the hierarchical modularity of the structural connectome using bifurcating dendrograms. Moving from fine to coarse (i.e., local to global) up the connectome's hierarchy, we computed the rate of decay of a new metric that hierarchically preferentially weighs the information exchange between two nodes in the same module. By computing "embeddedness"-the ratio between nodal efficiency and this decay rate, one could thus probe the relative scale-invariant information exchange efficiency of the human brain. Results suggest that regions that exhibit high embeddedness are those that comprise the limbic system, the default mode network, and the subcortical nuclei. This supports the presence of near-decomposability overall yet relative embeddedness in select areas of the brain. The areas we identified as highly embedded are varied in function but are arguably linked in the evolutionary role they play in memory, emotion and behavior.
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- 2015
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11. Ex vivo diffusion tensor MRI reflects microscopic structural remodeling associated with aging and disease progression in normal and cardiomyopathic Syrian hamsters
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Ming Lu, Allen Q. Ye, Wen Li, Joseph Molter, Jia Zhong, Suhanti Banerjee, and Xin Yu
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Pathology ,medicine.medical_specialty ,biology ,business.industry ,chemistry.chemical_element ,Dilated cardiomyopathy ,Calcium ,medicine.disease ,biology.organism_classification ,chemistry ,Fibrosis ,cardiovascular system ,medicine ,Molecular Medicine ,Radiology, Nuclear Medicine and imaging ,Ventricular remodeling ,business ,Pathological ,Spectroscopy ,Ex vivo ,Mesocricetus ,Diffusion MRI - Abstract
Dilated cardiomyopathy (DCM) is a major cause of mortality and morbidity in cardiac patients. Aging is often anignored etiology of pathological conditions. Quantification of DCM and aging associated cardiac structural remodel-ing is important in guiding and evaluating therapeutic interventions. Diffusion tensor magnetic resonance imaging(DTMRI) has recently been used for nondestructive characterization of three-dimensional myofiber structure. In thisstudy,weexploredthepotentialofDTMRIindelineatingmicroscopicstructuralremodelinginagingandDCMhearts.Six month (n¼10) and nine month old (n¼11) DCM (TO-2) hamsters and their age-matched controls (F1b) werecharacterized. Both aging and DCM hearts showed increased diffusivity and decreased diffusion anisotropy. DTMRIimages of DCM hearts also revealed a subgroup of imaging pixels characterized by decreased radial diffusivity andincreased FA. The location of these pixels showed qualitative agreement with regions of calcium depositiondetermined by X-ray CT imaging. Histological analysis confirmed expanded extracellular space in aging and DCMhearts as well as substantial calcium deposition in DCM hearts. These results suggest that DTMRI may provide anoninvasive technique to delineate structural remodeling associated with aging and DCM progression at the tissueand cellular level without the use of an exogenous contrast agent. Copyright 2009 John Wiley & Sons, Ltd.Keywords: aging; calcium deposition; diffusion tensor MRI; dilated cardiomyopathy; fibrosis
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- 2009
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12. Analysis of YFP(J16)-R6/2 reporter mice and postmortem brains reveals early pathology and increased vulnerability of callosal axons in Huntington's disease
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Jeffrey H. Kordower, Richard L. Magin, Ehsan Tavassoli, Gerardo Morfini, Rodolfo G. Gatto, Andrea Buenaventura, Scott T. Brady, Allen Q. Ye, Yaping Chu, and Steven D. Price
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Male ,Pathology ,medicine.medical_specialty ,Huntingtin ,Gene Expression ,Context (language use) ,Mice, Transgenic ,Biology ,Protein Aggregation, Pathological ,Severity of Illness Index ,Mice ,Huntington's disease ,Genes, Reporter ,Cortex (anatomy) ,Basal ganglia ,Genetics ,medicine ,Animals ,Humans ,Axon ,Molecular Biology ,Genetics (clinical) ,Aged ,Cerebral Cortex ,Neurons ,Serotonin Plasma Membrane Transport Proteins ,Microscopy, Confocal ,Brain ,General Medicine ,Articles ,Polyglutamine tract ,Middle Aged ,medicine.disease ,Axons ,medicine.anatomical_structure ,Huntington Disease ,nervous system ,Cerebral cortex ,Nerve Degeneration ,Female - Abstract
Cumulative evidence indicates that the onset and severity of Huntington's disease (HD) symptoms correlate with connectivity deficits involving specific neuronal populations within cortical and basal ganglia circuits. Brain imaging studies and pathological reports further associated these deficits with alterations in cerebral white matter structure and axonal pathology. However, whether axonopathy represents an early pathogenic event or an epiphenomenon in HD remains unknown, nor is clear the identity of specific neuronal populations affected. To directly evaluate early axonal abnormalities in the context of HD in vivo, we bred transgenic YFP(J16) with R6/2 mice, a widely used HD model. Diffusion tensor imaging and fluorescence microscopy studies revealed a marked degeneration of callosal axons long before the onset of motor symptoms. Accordingly, a significant fraction of YFP-positive cortical neurons in YFP(J16) mice cortex were identified as callosal projection neurons. Callosal axon pathology progressively worsened with age and was influenced by polyglutamine tract length in mutant huntingtin (mhtt). Degenerating axons were dissociated from microscopically visible mhtt aggregates and did not result from loss of cortical neurons. Interestingly, other axonal populations were mildly or not affected, suggesting differential vulnerability to mhtt toxicity. Validating these results, increased vulnerability of callosal axons was documented in the brains of HD patients. Observations here provide a structural basis for the alterations in cerebral white matter structure widely reported in HD patients. Collectively, our data demonstrate a dying-back pattern of degeneration for cortical projection neurons affected in HD, suggesting that axons represent an early and potentially critical target for mhtt toxicity.
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- 2015
13. Anisotropic fractional diffusion tensor imaging
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Richard L. Magin, Mark M. Meerschaert, and Allen Q. Ye
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Anomalous diffusion ,Aerospace Engineering ,01 natural sciences ,Article ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,Nuclear magnetic resonance ,Neuroimaging ,medicine ,General Materials Science ,Tensor ,Statistical physics ,0101 mathematics ,Anisotropy ,Physics ,medicine.diagnostic_test ,Mechanical Engineering ,Magnetic resonance imaging ,Fractional calculus ,010101 applied mathematics ,Mechanics of Materials ,Computer Science::Computer Vision and Pattern Recognition ,Automotive Engineering ,Diffusion MRI ,Tractography - Abstract
Traditional diffusion tensor imaging (DTI) maps brain structure by fitting a diffusion model to the magnitude of the electrical signal acquired in magnetic resonance imaging (MRI). Fractional DTI employs anomalous diffusion models to obtain a better fit to real MRI data, which can exhibit anomalous diffusion in both time and space. In this paper, we describe the challenge of developing and employing anisotropic fractional diffusion models for DTI. Since anisotropy is clearly present in the three-dimensional MRI signal response, such models hold great promise for improving brain imaging. We then propose some candidate models, based on stochastic theory.
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- 2015
14. Diffusion tensor MRI phantom exhibits anomalous diffusion
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Penny L. Hubbard Cristinacce, Feng-Lei Zhou, Ziying Yin, Allen Q. Ye, Geoffrey J. M. Parker, and Richard L. Magin
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Materials science ,Time Factors ,Anomalous diffusion ,Phantoms, Imaging ,Physics::Medical Physics ,Thermal diffusivity ,Magnetic Resonance Imaging ,Imaging phantom ,Article ,Mean squared displacement ,Diffusion ,Nuclear magnetic resonance ,Diffusion Tensor Imaging ,Fractional anisotropy ,Anisotropy ,Diffusion (business) ,Algorithms ,Diffusion MRI - Abstract
This paper reports diffusion weighted MRI measurements of cyclohexane in a novel diffusion tensor MRI phantom composed of hollow coaxial electrospun fibers (average diameter 10.2 μm). Recent studies of the phantom demonstrated its potential as a calibration standard at low b values (less than 1000 s/mm;sup2;/sup) for mean diffusivity and fractional anisotropy. In this paper, we extend the characterization of cyclohexane diffusion in this heterogeneous, anisotropic material to high b values (up to 5000 s/mm;sup2;/sup), where the apparent diffusive motion of the cyclohexane exhibits anomalous behavior (i.e., the molecular mean squared displacement increases with time raised to the fractional power 2α/β). Diffusion tensor MRI was performed at 9.4 T using an Agilent imaging scanner and the data fit to a fractional order Mittag-Leffler (generalized exponential) decay model. Diffusion along the fibers was found to be Gaussian (2α/β=l), while diffusion across the fibers was sub-diffusive (2α/β;l). Fiber tract reconstruction of the data was consistent with scanning electron micrograph images of the material. These studies suggest that this phantom material may be used to calibrate MR systems in both the normal (Gaussian) and anomalous diffusion regimes.
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- 2015
15. In Vivo Assessment of Oxygen Consumption via Deuterium Magnetic Resonance
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Jeffrey L. Duerk, Gheorghe D. Mateescu, Christopher A Flask, Bernadette O. Erokwu, and Allen Q. Ye
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medicine.diagnostic_test ,Apparent oxygen utilisation ,chemistry.chemical_element ,Magnetic resonance imaging ,Nuclear magnetic resonance spectroscopy ,Carbohydrate metabolism ,Oxygen ,Nuclear magnetic resonance ,chemistry ,Deuterium ,In vivo ,embryonic structures ,medicine ,Ex vivo - Abstract
We present a novel approach to simultaneously measure, in vivo, noninvasively, glucose and oxygen consumption via Deuterium Magnetic Resonance (DMR). Mice are administered deuteriated glucose by intravenous injection. The rate of formation of nascent (deuteriated) mitochondrial water is then measured via DMR. The rate of glucose metabolism and oxygen utilization is assessed by tracking their separate peaks in DMR spectra during dynamic scanning. Further studies will aim to validate these results by comparison with in vivo 17O-MRI (mitochondrial function), 13C-MRI and 19FDG-PET (glucose metabolism) and ex vivo 1H- and 2H-MR, as well as mass spectrometry.1
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- 2011
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